#nexus begin trees; tree sptree = (PGI,(OGI,(ST,(AGI,(GM,(MT,LJ)))))); end; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:43:34 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10336.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28059 C=0.20482 G=0.27202 T=0.24257 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 115 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2572.82241 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.38 sec) ] tree PAUP_1 = [&R] (((GM,GM),MT),LJ):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:43:38 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10531.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.20789 C=0.28483 G=0.24731 T=0.25998 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 196 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2911.64158 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.93 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:43:38 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10639.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29402 C=0.20640 G=0.24796 T=0.25161 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 128 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2691.27672 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.39 sec) ] tree PAUP_1 = [&R] ((GM,MT),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:48:34 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10641.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29623 C=0.19722 G=0.26987 T=0.23668 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 443 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1130 > Score of best tree(s) found = 6823.05656 > Number of trees retained = 1 > Time used = 01:00:02 (CPU time = 00:59:56.0) ] tree PAUP_1 = [&R] ((((AGI,AGI),((ST,ST),ST)),((((LJ,(MT,GM)),(GM,GM)),LJ),MT)),((OGI,OGI),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:44:41 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10649.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25538 C=0.22547 G=0.24020 T=0.27895 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 183 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 114 > Score of best tree(s) found = 2348.71418 > Number of trees retained = 1 > Time used = 00:01:03 (CPU time = 00:01:02.4) ] tree PAUP_1 = [&R] (((AGI,AGI),((AGI,GM),AGI)),(GM,(LJ,MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:45:19 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10702.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23300 C=0.27003 G=0.22088 T=0.27609 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 225 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 69 > Score of best tree(s) found = 2615.45300 > Number of trees retained = 1 > Time used = 38 sec (CPU time = 37.40 sec) ] tree PAUP_1 = [&R] ((((MT,MT),(GM,GM)),LJ),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:45:53 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl10838.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31759 C=0.17513 G=0.25253 T=0.25475 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 350 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 46 > Score of best tree(s) found = 4640.94828 > Number of trees retained = 1 > Time used = 33 sec (CPU time = 32.75 sec) ] tree PAUP_1 = [&R] (((GM,(MT,(GM,MT))),ST),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:46:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11019.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24772 C=0.21475 G=0.30437 T=0.23316 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 282 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 39 > Score of best tree(s) found = 4333.58729 > Number of trees retained = 1 > Time used = 23 sec (CPU time = 23.87 sec) ] tree PAUP_1 = [&R] (((((GM,GM),LJ),GM),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11038.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25146 C=0.22849 G=0.19465 T=0.32540 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 270 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 78 > Score of best tree(s) found = 3342.44518 > Number of trees retained = 1 > Time used = 00:01:02 (CPU time = 00:01:02.1) ] tree PAUP_1 = [&R] (((AGI,(LJ,(MT,GM))),ST),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11234.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27446 C=0.23931 G=0.26302 T=0.22321 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 127 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2040.34139 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.49 sec) ] tree PAUP_1 = [&R] ((GM,AGI),(MT,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:21 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11347.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26060 C=0.23600 G=0.21952 T=0.28388 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 121 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2529.84860 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.40 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:25 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11559.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29444 C=0.20067 G=0.24343 T=0.26146 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 200 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2884.85109 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.89 sec) ] tree PAUP_1 = [&R] (((GM,MT),GM),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:26 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11566.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29775 C=0.17962 G=0.24546 T=0.27717 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 135 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3083.99409 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.44 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:31 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11726.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28656 C=0.22036 G=0.24967 T=0.24341 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 79 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2176.89225 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.95 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:11:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11728.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27382 C=0.21582 G=0.21555 T=0.29481 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 309 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 684 > Score of best tree(s) found = 3844.52816 > Number of trees retained = 1 > Time used = 00:17:33 (CPU time = 00:17:30.4) ] tree PAUP_1 = [&R] (((((LJ,MT),((GM,GM),GM)),MT),((ST,ST),ST)),(((AGI,AGI),AGI),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:31 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11781.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28218 C=0.19480 G=0.23713 T=0.28589 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 155 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3237.26182 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.62 sec) ] tree PAUP_1 = [&R] (((GM,MT),AGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:32 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11828.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25629 C=0.20472 G=0.22585 T=0.31314 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 113 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2150.64262 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.38 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:32 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl11847.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29360 C=0.15642 G=0.28382 T=0.26616 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 98 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2113.31420 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.31 sec) ] tree PAUP_1 = [&R] (((GM,MT),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:33 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl1214.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27426 C=0.20007 G=0.24367 T=0.28200 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 138 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2303.65328 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.51 sec) ] tree PAUP_1 = [&R] ((ST,ST),(MT,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:47:49 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl1221.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30577 C=0.20495 G=0.19990 T=0.28938 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 251 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 35 > Score of best tree(s) found = 3494.85026 > Number of trees retained = 1 > Time used = 15 sec (CPU time = 15.49 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),((GM,GM),MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:49:10 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl12460.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28964 C=0.19872 G=0.26386 T=0.24778 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 451 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 6169.36281 > Number of trees retained = 1 > Time used = 00:01:20 (CPU time = 00:01:20.2) ] tree PAUP_1 = [&R] ((((AGI,AGI),(ST,MT)),PGI),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:12:47 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl12473.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23648 C=0.22905 G=0.21287 T=0.32160 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 509 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 260 > Score of best tree(s) found = 7178.01886 > Number of trees retained = 1 > Time used = 00:08:44 (CPU time = 00:08:43.2) ] tree PAUP_1 = [&R] ((PGI,PGI),(((GM,MT),((AGI,AGI),AGI)),((ST,ST),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 13:23:03 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl12863.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28506 C=0.21966 G=0.26180 T=0.23347 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 321 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3868 > Score of best tree(s) found = 6338.57269 > Number of trees retained = 1 > Time used = 03:49:36 (CPU time = 03:49:11.5) ] tree PAUP_1 = [&R] (((((((((((AGI,AGI),AGI),AGI),ST),(ST,ST)),(((GM,GM),GM),LJ)),((OGI,OGI),(OGI,OGI))),GM),(LJ,MT)),(MT,GM)),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:49:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl12956.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27882 C=0.19601 G=0.24230 T=0.28287 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 181 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5875.90394 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.58 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),(GM,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 16:39:52 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13000.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25941 C=0.21100 G=0.27455 T=0.25504 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 328 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2961 > Score of best tree(s) found = 5610.20630 > Number of trees retained = 1 > Time used = 02:56:41 (CPU time = 02:56:19.4) ] tree PAUP_1 = [&R] (((PGI,PGI),((ST,(ST,ST)),ST)),(((((((GM,GM),GM),GM),MT),(MT,MT)),(AGI,AGI)),((AGI,AGI),(((OGI,OGI),OGI),OGI)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sat Mar 25 04:54:58 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13024.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28806 C=0.19146 G=0.26175 T=0.25872 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 590 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 498 > Score of best tree(s) found = 7927.61740 > Number of trees retained = 1 > Time used = 00:25:33 (CPU time = 00:25:30.1) ] tree PAUP_1 = [&R] (((((GM,LJ),GM),MT),(((OGI,OGI),(PGI,PGI)),(ST,ST))),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:49:12 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl1317.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25000 C=0.21605 G=0.20707 T=0.32688 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 133 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2787.66404 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.56 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:49:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13199.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28865 C=0.17021 G=0.25532 T=0.28582 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 158 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 16 > Score of best tree(s) found = 2127.18680 > Number of trees retained = 1 > Time used = 5 sec (CPU time = 5.00 sec) ] tree PAUP_1 = [&R] (((GM,MT),AGI),(PGI,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:49:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13219.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24504 C=0.24207 G=0.23786 T=0.27502 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 227 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 72 > Score of best tree(s) found = 2465.13687 > Number of trees retained = 1 > Time used = 33 sec (CPU time = 33.35 sec) ] tree PAUP_1 = [&R] ((LJ,(MT,GM)),(((GM,GM),MT),LJ)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:49:52 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl1331.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27336 C=0.20066 G=0.26091 T=0.26506 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 206 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5780.16217 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.69 sec) ] tree PAUP_1 = [&R] ((GM,MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:55:15 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13360.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28971 C=0.20440 G=0.25272 T=0.25317 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 830 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 128 > Score of best tree(s) found = 10661.14046 > Number of trees retained = 1 > Time used = 00:05:21 (CPU time = 00:05:20.2) ] tree PAUP_1 = [&R] ((AGI,((LJ,MT),(GM,MT))),(ST,(OGI,OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:55:22 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13490.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30821 C=0.21183 G=0.23123 T=0.24873 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 275 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 5133.37360 > Number of trees retained = 1 > Time used = 7 sec (CPU time = 6.66 sec) ] tree PAUP_1 = [&R] ((((GM,MT),ST),OGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sat Mar 25 05:28:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13587.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28363 C=0.21059 G=0.24200 T=0.26378 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 400 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 604 > Score of best tree(s) found = 5010.41394 > Number of trees retained = 1 > Time used = 00:26:04 (CPU time = 00:26:01.3) ] tree PAUP_1 = [&R] ((((AGI,AGI),((GM,GM),MT)),ST),(((((LJ,MT),GM),LJ),ST),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:55:23 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13668.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29127 C=0.20265 G=0.23895 T=0.26714 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 151 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3656.99243 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.55 sec) ] tree PAUP_1 = [&R] (((GM,GM),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Sat Mar 25 07:09:19 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl13925.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31524 C=0.18786 G=0.25746 T=0.23944 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 393 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 373 > Score of best tree(s) found = 5242.45180 > Number of trees retained = 1 > Time used = 00:11:08 (CPU time = 00:11:07.1) ] tree PAUP_1 = [&R] (((AGI,AGI),(ST,ST)),((GM,(LJ,(MT,MT))),((GM,GM),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:57:21 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl14035.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28253 C=0.19362 G=0.23286 T=0.29099 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 180 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4263.61006 > Number of trees retained = 1 > Time used = 00:01:58 (CPU time = 00:01:58.0) ] tree PAUP_1 = [&R] (((GM,MT),ST),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:57:22 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl14044.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28414 C=0.18950 G=0.23569 T=0.29067 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 131 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3001.66030 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.38 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 06:58:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl14094.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28342 C=0.22709 G=0.23422 T=0.25526 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 259 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 66 > Score of best tree(s) found = 3433.56274 > Number of trees retained = 1 > Time used = 47 sec (CPU time = 46.62 sec) ] tree PAUP_1 = [&R] (((((MT,MT),GM),(GM,LJ)),ST),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:01:04 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl14656.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31001 C=0.19040 G=0.21508 T=0.28451 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 236 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4699.01422 > Number of trees retained = 1 > Time used = 5 sec (CPU time = 4.99 sec) ] tree PAUP_1 = [&R] ((((GM,LJ),AGI),OGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:00:59 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl146.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29575 C=0.19592 G=0.22233 T=0.28601 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 266 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 196 > Score of best tree(s) found = 3106.29279 > Number of trees retained = 1 > Time used = 00:02:49 (CPU time = 00:02:47.9) ] tree PAUP_1 = [&R] (((((GM,GM),MT),(GM,MT)),ST),((AGI,AGI),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sat Mar 25 08:19:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl15009.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.21583 C=0.22531 G=0.25567 T=0.30319 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 1057 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 534 > Score of best tree(s) found = 14916.21360 > Number of trees retained = 1 > Time used = 00:53:28 (CPU time = 00:53:25.1) ] tree PAUP_1 = [&R] (((((GM,LJ),MT),ST),(((PGI,PGI),ST),AGI)),(GM,(OGI,(OGI,OGI)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:01:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl15037.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25242 C=0.18448 G=0.22784 T=0.33527 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 227 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 14 > Score of best tree(s) found = 2774.11205 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.50 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:01:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl15627.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27314 C=0.19736 G=0.25292 T=0.27658 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 199 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5505.91068 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.59 sec) ] tree PAUP_1 = [&R] ((ST,ST),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:01:14 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl15896.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25639 C=0.20643 G=0.23364 T=0.30354 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 220 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 3378.32726 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.76 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:01:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl15958.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26964 C=0.24841 G=0.24805 T=0.23390 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 146 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2026.01270 > Number of trees retained = 1 > Time used = 3 sec (CPU time = 3.05 sec) ] tree PAUP_1 = [&R] (((GM,(LJ,MT)),AGI),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:02:39 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl16447.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23500 C=0.26466 G=0.28291 T=0.21743 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 254 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 106 > Score of best tree(s) found = 2930.10255 > Number of trees retained = 1 > Time used = 00:01:21 (CPU time = 00:01:20.9) ] tree PAUP_1 = [&R] ((((LJ,MT),(GM,GM)),(ST,ST)),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:02:39 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl16715.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31161 C=0.19016 G=0.23271 T=0.26551 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 103 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1815.78752 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.50 sec) ] tree PAUP_1 = [&R] (((GM,MT),PGI),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:07:22 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl16758.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23664 C=0.23953 G=0.29913 T=0.22470 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 359 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 227 > Score of best tree(s) found = 4746.65517 > Number of trees retained = 1 > Time used = 00:04:42 (CPU time = 00:04:41.1) ] tree PAUP_1 = [&R] (((((GM,GM),LJ),((GM,LJ),MT)),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:09:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl16839.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26682 C=0.21766 G=0.25575 T=0.25977 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 382 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 114 > Score of best tree(s) found = 5418.68575 > Number of trees retained = 1 > Time used = 00:01:48 (CPU time = 00:01:48.2) ] tree PAUP_1 = [&R] ((((GM,LJ),MT),(ST,ST)),((AGI,AGI),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 07:32:29 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl16926.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26347 C=0.23938 G=0.25781 T=0.23933 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 588 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 2873 > Score of best tree(s) found = 11951.98326 > Number of trees retained = 1 > Time used = 06:00:01 (CPU time = 05:59:00.4) ] tree PAUP_1 = [&R] (((((OGI,OGI),OGI),(OGI,((((AGI,AGI),AGI),((ST,ST),GM)),(PGI,PGI)))),(OGI,OGI)),(((((((AGI,AGI),AGI),(ST,ST)),MT),LJ),GM),(GM,(LJ,MT)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:09:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17064.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26991 C=0.24726 G=0.19592 T=0.28690 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 100 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1830.79512 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.37 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:11:36 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17188.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26416 C=0.20156 G=0.26663 T=0.26765 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 280 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 122 > Score of best tree(s) found = 3219.84949 > Number of trees retained = 1 > Time used = 00:02:24 (CPU time = 00:02:23.3) ] tree PAUP_1 = [&R] ((((GM,MT),AGI),((ST,ST),PGI)),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 07:59:30 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17219.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26143 C=0.21239 G=0.25039 T=0.27579 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 491 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 335 > Score of best tree(s) found = 6340.77654 > Number of trees retained = 1 > Time used = 00:16:32 (CPU time = 00:16:31.2) ] tree PAUP_1 = [&R] ((((AGI,AGI),MT),PGI),(((OGI,((OGI,OGI),OGI)),ST),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:09:33 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17302.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25463 C=0.22165 G=0.24341 T=0.28032 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 482 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 305 > Score of best tree(s) found = 6280.42293 > Number of trees retained = 1 > Time used = 00:10:01 (CPU time = 00:09:40.8) ] tree PAUP_1 = [&R] (((AGI,AGI),PGI),(((((GM,GM),MT),LJ),MT),(ST,OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:24:47 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17571.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30353 C=0.19002 G=0.23465 T=0.27179 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 380 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 522 > Score of best tree(s) found = 4603.95410 > Number of trees retained = 1 > Time used = 00:15:12 (CPU time = 00:15:10.1) ] tree PAUP_1 = [&R] ((((((GM,GM),MT),ST),(ST,ST)),(GM,MT)),(((AGI,AGI),AGI),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sat Mar 25 23:30:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17703.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28980 C=0.21343 G=0.22776 T=0.26901 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 501 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2905 > Score of best tree(s) found = 8095.12355 > Number of trees retained = 1 > Time used = 03:56:22 (CPU time = 03:55:57.7) ] tree PAUP_1 = [&R] (((((AGI,AGI),((GM,MT),LJ)),((ST,ST),(((GM,MT),(((GM,GM),MT),(LJ,LJ))),OGI))),((ST,ST),AGI)),((PGI,PGI),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:14:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl17819.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26866 C=0.22882 G=0.22786 T=0.27466 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 414 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 118 > Score of best tree(s) found = 5155.84640 > Number of trees retained = 1 > Time used = 00:02:31 (CPU time = 00:02:30.9) ] tree PAUP_1 = [&R] (((AGI,AGI),((GM,(LJ,MT)),ST)),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:14:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl18180.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31082 C=0.21781 G=0.21781 T=0.25356 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 119 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2294.83010 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.39 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:36:29 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl18481.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22312 C=0.24404 G=0.25700 T=0.27584 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 687 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 254 > Score of best tree(s) found = 9739.94900 > Number of trees retained = 1 > Time used = 00:11:40 (CPU time = 00:11:38.5) ] tree PAUP_1 = [&R] (((((AGI,AGI),AGI),((GM,LJ),MT)),(ST,ST)),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:14:24 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl18685.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22675 C=0.19013 G=0.21765 T=0.36548 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 183 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 2948.39509 > Number of trees retained = 1 > Time used = 14 sec (CPU time = 14.33 sec) ] tree PAUP_1 = [&R] ((((GM,MT),LJ),GM),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 10:08:23 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl18771.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29295 C=0.21428 G=0.27562 T=0.21715 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 444 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1448 > Score of best tree(s) found = 7031.04245 > Number of trees retained = 1 > Time used = 01:31:51 (CPU time = 01:31:40.5) ] tree PAUP_1 = [&R] (((AGI,AGI),(PGI,PGI)),((((OGI,OGI),OGI),((GM,MT),((GM,MT),((LJ,MT),GM)))),((ST,ST),ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:44:31 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl18778.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28937 C=0.20215 G=0.23956 T=0.26892 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 558 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1018 > Score of best tree(s) found = 8235.45364 > Number of trees retained = 1 > Time used = 01:07:13 (CPU time = 01:07:05.9) ] tree PAUP_1 = [&R] (((GM,GM),(ST,ST)),(MT,(GM,(LJ,(LJ,((((MT,MT),MT),MT),(MT,MT))))))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:14:47 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl18904.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28669 C=0.20375 G=0.23941 T=0.27016 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 349 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 5439.57723 > Number of trees retained = 1 > Time used = 22 sec (CPU time = 22.59 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),(((GM,MT),ST),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 12:24:07 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl19036.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29439 C=0.22948 G=0.27225 T=0.20388 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 463 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 841 > Score of best tree(s) found = 6006.70624 > Number of trees retained = 1 > Time used = 00:39:33 (CPU time = 00:39:29.2) ] tree PAUP_1 = [&R] (((((GM,MT),LJ),GM),((OGI,OGI),OGI)),((AGI,AGI),((ST,(ST,ST)),(ST,ST)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 14:51:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl19150.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27459 C=0.22432 G=0.23025 T=0.27084 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 433 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2145 > Score of best tree(s) found = 6577.93997 > Number of trees retained = 1 > Time used = 02:27:39 (CPU time = 02:27:21.0) ] tree PAUP_1 = [&R] (((((((LJ,LJ),(((GM,GM),GM),(MT,(MT,MT)))),(OGI,OGI)),(((PGI,PGI),PGI),(ST,ST))),AGI),(AGI,AGI)),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:14:47 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl19282.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23121 C=0.26590 G=0.19769 T=0.30520 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 81 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1848.01024 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.28 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:15:32 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl19452.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26005 C=0.21334 G=0.25727 T=0.26934 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 577 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 12482.00233 > Number of trees retained = 1 > Time used = 44 sec (CPU time = 43.36 sec) ] tree PAUP_1 = [&R] (((OGI,OGI),OGI),((AGI,AGI),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:20:02 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl19643.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28585 C=0.20249 G=0.24368 T=0.26798 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 320 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 234 > Score of best tree(s) found = 4153.63976 > Number of trees retained = 1 > Time used = 00:04:29 (CPU time = 00:04:28.6) ] tree PAUP_1 = [&R] (((AGI,AGI),PGI),((((MT,MT),LJ),(GM,GM)),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:20:03 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl19741.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28865 C=0.20602 G=0.23964 T=0.26569 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 111 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5069.01790 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.45 sec) ] tree PAUP_1 = [&R] (((GM,GM),MT),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:20:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl20207.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.32860 C=0.18147 G=0.26288 T=0.22706 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 194 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 2362.00298 > Number of trees retained = 1 > Time used = 13 sec (CPU time = 13.19 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),((ST,ST),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:20:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl20247.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.33511 C=0.15689 G=0.17067 T=0.33733 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 102 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1511.29006 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] (((GM,MT),AGI),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:20:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl2042.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24335 C=0.20190 G=0.20684 T=0.34791 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 118 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1964.36408 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.38 sec) ] tree PAUP_1 = [&R] (((LJ,MT),GM),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:21:04 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl20467.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29958 C=0.18220 G=0.23447 T=0.28375 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 233 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30 > Score of best tree(s) found = 2576.51695 > Number of trees retained = 1 > Time used = 47 sec (CPU time = 46.34 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),(GM,MT)),(ST,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:21:07 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl20700.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.21375 C=0.23679 G=0.21951 T=0.32995 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 130 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2029.71803 > Number of trees retained = 1 > Time used = 3 sec (CPU time = 2.65 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:21:14 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl20804.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.34162 C=0.18355 G=0.23097 T=0.24386 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 320 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 5288.93762 > Number of trees retained = 1 > Time used = 7 sec (CPU time = 6.83 sec) ] tree PAUP_1 = [&R] ((GM,PGI),(AGI,(OGI,ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 15:27:04 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl21023.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23591 C=0.24726 G=0.26081 T=0.25602 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 634 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 376 > Score of best tree(s) found = 9808.87737 > Number of trees retained = 1 > Time used = 00:18:00 (CPU time = 00:17:57.1) ] tree PAUP_1 = [&R] ((((((GM,OGI),LJ),(MT,MT)),(AGI,AGI)),(ST,ST)),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:21:15 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl21524.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27208 C=0.21756 G=0.23682 T=0.27354 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 117 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3 > Score of best tree(s) found = 4017.70908 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.50 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:21:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl21617.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27697 C=0.19716 G=0.22808 T=0.29779 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 167 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3 > Score of best tree(s) found = 2782.06917 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.86 sec) ] tree PAUP_1 = [&R] (AGI,((GM,GM),MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:24:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl21654.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28380 C=0.21360 G=0.24941 T=0.25319 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 395 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 130 > Score of best tree(s) found = 4520.84974 > Number of trees retained = 1 > Time used = 00:03:00 (CPU time = 00:02:59.4) ] tree PAUP_1 = [&R] (((OGI,OGI),PGI),((((GM,GM),MT),ST),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:24:21 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl21807.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27904 C=0.19552 G=0.23910 T=0.28634 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 158 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2956.80853 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.95 sec) ] tree PAUP_1 = [&R] (((GM,GM),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:24:27 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl21859.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26609 C=0.21764 G=0.25206 T=0.26421 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 260 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4932.97813 > Number of trees retained = 1 > Time used = 6 sec (CPU time = 5.38 sec) ] tree PAUP_1 = [&R] (((ST,ST),(GM,MT)),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 05:30:29 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl22015.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28998 C=0.18986 G=0.24729 T=0.27287 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 523 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 2630 > Score of best tree(s) found = 8400.34496 > Number of trees retained = 3 > Time used = 06:00:03 (CPU time = 05:58:50.5) ] tree PAUP_1 = [&R] ((((((((AGI,AGI),(((GM,GM),MT),LJ)),ST),(OGI,OGI)),PGI),PGI),((((AGI,AGI),ST),(((GM,LJ),MT),MT)),OGI)),((AGI,ST),(GM,MT))):0.3333; tree PAUP_2 = [&R] ((((((((AGI,AGI),(((GM,GM),MT),LJ)),ST),(OGI,OGI)),PGI),((((AGI,AGI),ST),(((GM,LJ),MT),MT)),OGI)),PGI),((AGI,ST),(GM,MT))):0.3333; tree PAUP_3 = [&R] (((((((AGI,AGI),(((GM,GM),MT),LJ)),ST),(OGI,OGI)),PGI),(((((AGI,AGI),ST),(((GM,LJ),MT),MT)),OGI),PGI)),((AGI,ST),(GM,MT))):0.3333; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:24:27 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl22054.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24362 C=0.24017 G=0.23499 T=0.28123 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 101 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2014.81699 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:24:28 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl2213.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26483 C=0.22282 G=0.23505 T=0.27729 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 237 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 9804.05117 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.78 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:24:29 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl22200.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.20244 C=0.20332 G=0.32766 T=0.26658 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 94 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1501.56973 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] ((LJ,MT),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 17:38:19 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl22344.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24730 C=0.22323 G=0.26566 T=0.26380 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 854 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1265 > Score of best tree(s) found = 12139.17630 > Number of trees retained = 1 > Time used = 02:11:08 (CPU time = 02:10:56.1) ] tree PAUP_1 = [&R] ((((AGI,AGI),((GM,LJ),MT)),(OGI,ST)),(((AGI,AGI),((GM,(LJ,MT)),ST)),((OGI,OGI),OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:30:27 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl22554.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28023 C=0.20491 G=0.25557 T=0.25929 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 438 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1176 > Score of best tree(s) found = 5527.14412 > Number of trees retained = 1 > Time used = 00:52:05 (CPU time = 00:52:00.4) ] tree PAUP_1 = [&R] (((((GM,GM),GM),GM),(((GM,LJ),MT),MT)),((((AGI,AGI),((GM,MT),MT)),ST),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:25:08 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl22798.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26978 C=0.20191 G=0.24882 T=0.27948 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 251 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 5027.81037 > Number of trees retained = 1 > Time used = 38 sec (CPU time = 38.17 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),ST),(MT,LJ)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:26:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23032.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27558 C=0.19160 G=0.25085 T=0.28197 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 369 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 5072.96204 > Number of trees retained = 1 > Time used = 52 sec (CPU time = 51.95 sec) ] tree PAUP_1 = [&R] (((GM,MT),(GM,LJ)),(ST,(AGI,AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:26:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23191.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28499 C=0.18699 G=0.27782 T=0.25020 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 190 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 35 > Score of best tree(s) found = 2553.33817 > Number of trees retained = 1 > Time used = 16 sec (CPU time = 15.58 sec) ] tree PAUP_1 = [&R] ((((LJ,(MT,GM)),AGI),ST),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:26:34 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23200.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30955 C=0.19867 G=0.24694 T=0.24484 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 225 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 40 > Score of best tree(s) found = 3513.95519 > Number of trees retained = 1 > Time used = 18 sec (CPU time = 17.37 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,(MT,MT))),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:30:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23212.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.21369 C=0.21233 G=0.21096 T=0.36302 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 299 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 188 > Score of best tree(s) found = 3895.27248 > Number of trees retained = 1 > Time used = 00:03:36 (CPU time = 00:03:35.6) ] tree PAUP_1 = [&R] (((((LJ,MT),GM),ST),(PGI,PGI)),((GM,MT),GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:30:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23259.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30971 C=0.17861 G=0.21697 T=0.29472 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 118 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2807.48133 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.41 sec) ] tree PAUP_1 = [&R] (((GM,MT),OGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:30:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl2335.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26404 C=0.22733 G=0.24348 T=0.26515 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 293 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 5447.37167 > Number of trees retained = 1 > Time used = 6 sec (CPU time = 5.35 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:30:36 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23648.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26365 C=0.18950 G=0.26222 T=0.28463 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 283 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30 > Score of best tree(s) found = 4876.40510 > Number of trees retained = 1 > Time used = 18 sec (CPU time = 18.01 sec) ] tree PAUP_1 = [&R] (((ST,ST),(GM,MT)),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 12:23:14 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23770.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29920 C=0.19186 G=0.27136 T=0.23758 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 1120 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 1688 > Score of best tree(s) found = 18367.85890 > Number of trees retained = 1 > Time used = 06:00:02 (CPU time = 05:59:10.5) ] tree PAUP_1 = [&R] ((((((AGI,AGI),AGI),AGI),((OGI,OGI),OGI)),(((GM,MT),GM),((ST,ST),ST))),(((AGI,((MT,MT),(ST,ST))),PGI),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:31:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl23903.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28261 C=0.21337 G=0.24074 T=0.26329 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 270 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 3240.07131 > Number of trees retained = 1 > Time used = 43 sec (CPU time = 43.47 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),((GM,(LJ,MT)),(ST,ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:55:57 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24064.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27387 C=0.20975 G=0.27714 T=0.23924 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 344 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 681 > Score of best tree(s) found = 5060.24456 > Number of trees retained = 1 > Time used = 00:25:28 (CPU time = 00:25:27.4) ] tree PAUP_1 = [&R] (((((AGI,AGI),AGI),AGI),(ST,ST)),((((GM,GM),GM),LJ),((MT,MT),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:32:34 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl2407.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28728 C=0.21251 G=0.26616 T=0.23405 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 226 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 119 > Score of best tree(s) found = 2789.51089 > Number of trees retained = 1 > Time used = 00:01:14 (CPU time = 00:01:13.8) ] tree PAUP_1 = [&R] ((((GM,MT),LJ),(GM,MT)),((GM,GM),MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:32:54 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24140.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27207 C=0.18280 G=0.25520 T=0.28993 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 273 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 36 > Score of best tree(s) found = 4104.25276 > Number of trees retained = 1 > Time used = 20 sec (CPU time = 19.70 sec) ] tree PAUP_1 = [&R] ((((GM,MT),GM),ST),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:32:55 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24244.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29244 C=0.18693 G=0.25958 T=0.26104 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 115 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 4 > Score of best tree(s) found = 2098.34998 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.53 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:33:41 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24361.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27860 C=0.23812 G=0.20947 T=0.27380 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 325 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 4298.39582 > Number of trees retained = 1 > Time used = 45 sec (CPU time = 45.03 sec) ] tree PAUP_1 = [&R] ((((GM,MT),LJ),(LJ,MT)),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 19:51:26 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24422.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28747 C=0.19852 G=0.28231 T=0.23170 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 677 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 842 > Score of best tree(s) found = 9545.61346 > Number of trees retained = 1 > Time used = 00:55:25 (CPU time = 00:55:24.4) ] tree PAUP_1 = [&R] ((((((MT,LJ),(GM,GM)),(LJ,GM)),MT),(AGI,AGI)),((OGI,OGI),((ST,ST),ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:34:33 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24434.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27950 C=0.19143 G=0.22958 T=0.29949 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 362 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 5055.29291 > Number of trees retained = 1 > Time used = 51 sec (CPU time = 51.58 sec) ] tree PAUP_1 = [&R] ((GM,(MT,GM)),((AGI,AGI),(AGI,AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:34:34 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24521.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22574 C=0.27162 G=0.25487 T=0.24776 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 129 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3150.92937 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.42 sec) ] tree PAUP_1 = [&R] ((LJ,MT),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:37:35 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24851.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25529 C=0.22858 G=0.26317 T=0.25296 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 283 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 217 > Score of best tree(s) found = 3651.49742 > Number of trees retained = 1 > Time used = 00:03:01 (CPU time = 00:03:00.7) ] tree PAUP_1 = [&R] ((GM,((LJ,(GM,GM)),MT)),(((ST,ST),ST),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:37:38 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl24854.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27075 C=0.18351 G=0.18244 T=0.36330 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 121 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2258.27989 > Number of trees retained = 1 > Time used = 3 sec (CPU time = 2.51 sec) ] tree PAUP_1 = [&R] ((((LJ,MT),GM),AGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:37:39 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl25252.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25155 C=0.19293 G=0.21710 T=0.33842 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 128 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 4 > Score of best tree(s) found = 5481.39531 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.74 sec) ] tree PAUP_1 = [&R] (((AGI,OGI),LJ),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:37:45 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl25400.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23331 C=0.21695 G=0.21829 T=0.33146 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 219 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2733.76535 > Number of trees retained = 1 > Time used = 6 sec (CPU time = 5.36 sec) ] tree PAUP_1 = [&R] (((GM,MT),ST),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:29 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl25482.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26605 C=0.23781 G=0.23141 T=0.26473 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 236 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 2796.61495 > Number of trees retained = 1 > Time used = 44 sec (CPU time = 43.75 sec) ] tree PAUP_1 = [&R] ((((MT,MT),(GM,GM)),LJ),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:35 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl25735.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23268 C=0.26587 G=0.27058 T=0.23087 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 254 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 3993.93010 > Number of trees retained = 1 > Time used = 5 sec (CPU time = 5.03 sec) ] tree PAUP_1 = [&R] ((((GM,GM),LJ),MT),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 20:17:35 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl25972.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28886 C=0.22774 G=0.22538 T=0.25801 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 849 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 392 > Score of best tree(s) found = 10301.15740 > Number of trees retained = 1 > Time used = 00:26:06 (CPU time = 00:26:05.4) ] tree PAUP_1 = [&R] (((((OGI,OGI),OGI),OGI),(GM,MT)),(((AGI,AGI),(AGI,AGI)),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26357.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28595 C=0.21879 G=0.23707 T=0.25819 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 303 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4888.56977 > Number of trees retained = 1 > Time used = 15 sec (CPU time = 15.42 sec) ] tree PAUP_1 = [&R] (((GM,MT),AGI),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 22:45:26 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl26386.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22886 C=0.25191 G=0.28119 T=0.23804 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 383 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 667 > Score of best tree(s) found = 5683.74746 > Number of trees retained = 1 > Time used = 00:36:52 (CPU time = 00:36:52.3) ] tree PAUP_1 = [&R] ((((AGI,(AGI,AGI)),((ST,ST),ST)),(MT,MT)),(LJ,((GM,GM),(GM,OGI)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26400.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26411 C=0.19717 G=0.24994 T=0.28878 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 173 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3735.10515 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.61 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),ST),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:52 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26527.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23549 C=0.26819 G=0.21586 T=0.28046 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 96 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1699.81984 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.35 sec) ] tree PAUP_1 = [&R] ((LJ,MT),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:55 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26563.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28285 C=0.19061 G=0.26424 T=0.26230 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 165 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 3872.99492 > Number of trees retained = 1 > Time used = 3 sec (CPU time = 2.91 sec) ] tree PAUP_1 = [&R] ((((GM,MT),GM),LJ),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:38:56 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26600.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28946 C=0.20162 G=0.22757 T=0.28135 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 157 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2927.85912 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.65 sec) ] tree PAUP_1 = [&R] ((LJ,MT),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:39:34 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26602.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29346 C=0.20686 G=0.25854 T=0.24114 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 349 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 5417.75681 > Number of trees retained = 1 > Time used = 37 sec (CPU time = 37.36 sec) ] tree PAUP_1 = [&R] (((GM,OGI),ST),((AGI,AGI),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:41:55 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26711.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26817 C=0.20827 G=0.26647 T=0.25708 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 660 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 77 > Score of best tree(s) found = 8874.36814 > Number of trees retained = 1 > Time used = 00:02:20 (CPU time = 00:02:19.8) ] tree PAUP_1 = [&R] (((GM,(GM,MT)),ST),(AGI,(OGI,OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:42:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26714.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30309 C=0.18482 G=0.25650 T=0.25560 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 211 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2667.91465 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.13 sec) ] tree PAUP_1 = [&R] ((AGI,(GM,MT)),(ST,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 23:14:00 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl26731.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29868 C=0.23534 G=0.24045 T=0.22552 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 319 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 649 > Score of best tree(s) found = 3782.71759 > Number of trees retained = 1 > Time used = 00:28:32 (CPU time = 00:28:31.8) ] tree PAUP_1 = [&R] ((((LJ,LJ),((MT,((GM,GM),MT)),((GM,GM),GM))),(AGI,AGI)),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:46:29 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26745.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29867 C=0.16962 G=0.27354 T=0.25816 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 685 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 114 > Score of best tree(s) found = 9569.81085 > Number of trees retained = 1 > Time used = 00:04:27 (CPU time = 00:04:26.9) ] tree PAUP_1 = [&R] ((((AGI,AGI),ST),(GM,MT)),(ST,(PGI,PGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:45:31 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl26865.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27898 C=0.20717 G=0.24208 T=0.27177 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 1214 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 607 > Score of best tree(s) found = 17865.39699 > Number of trees retained = 1 > Time used = 02:29:15 (CPU time = 02:29:07.8) ] tree PAUP_1 = [&R] (((((GM,GM),(LJ,MT)),((LJ,MT),GM)),(AGI,AGI)),((MT,ST),(ST,ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:46:30 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl26924.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27202 C=0.21952 G=0.26097 T=0.24750 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 148 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 4312.53171 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.59 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:46:30 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl27083.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30482 C=0.19772 G=0.22856 T=0.26891 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 181 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3844.04212 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.66 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),(MT,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:47:35 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl27468.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.21062 C=0.25754 G=0.24359 T=0.28825 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 385 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30 > Score of best tree(s) found = 5232.27005 > Number of trees retained = 1 > Time used = 26 sec (CPU time = 25.35 sec) ] tree PAUP_1 = [&R] (((GM,GM),(LJ,MT)),(OGI,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:47:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl274.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28507 C=0.21610 G=0.25689 T=0.24194 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 242 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 2891.72232 > Number of trees retained = 1 > Time used = 39 sec (CPU time = 37.85 sec) ] tree PAUP_1 = [&R] (((ST,ST),OGI),((GM,MT),(AGI,AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:48:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl27519.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22288 C=0.27249 G=0.25017 T=0.25446 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 286 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 3996.41548 > Number of trees retained = 1 > Time used = 45 sec (CPU time = 44.25 sec) ] tree PAUP_1 = [&R] (((ST,ST),(ST,ST)),((GM,LJ),MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:24:14 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl27837.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25330 C=0.23172 G=0.25796 T=0.25702 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 793 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 693 > Score of best tree(s) found = 28244.22832 > Number of trees retained = 1 > Time used = 06:00:29 (CPU time = 05:59:55.7) ] tree PAUP_1 = [&R] (((((((AGI,AGI),AGI),((((GM,GM),LJ),((MT,MT),MT)),(ST,ST))),((AGI,(ST,ST)),((LJ,MT),GM))),((AGI,AGI),((AGI,AGI),ST))),((((AGI,ST),OGI),MT),(GM,MT))),(((((GM,LJ),PGI),(PGI,PGI)),(((PGI,PGI),PGI),PGI)),(((((OGI,OGI),OGI),OGI),GM),((GM,MT),GM)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:54:35 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl27859.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26120 C=0.17719 G=0.29943 T=0.26218 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 469 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 231 > Score of best tree(s) found = 5136.19899 > Number of trees retained = 1 > Time used = 00:06:14 (CPU time = 00:06:12.9) ] tree PAUP_1 = [&R] ((((((GM,GM),GM),LJ),MT),MT),(ST,(AGI,AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:54:40 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl27918.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25971 C=0.18902 G=0.24511 T=0.30616 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 174 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2446.18810 > Number of trees retained = 1 > Time used = 5 sec (CPU time = 5.11 sec) ] tree PAUP_1 = [&R] (((LJ,MT),ST),(GM,LJ)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 20:50:13 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl27921.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26431 C=0.23015 G=0.23361 T=0.27193 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 467 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1307 > Score of best tree(s) found = 6677.79732 > Number of trees retained = 1 > Time used = 02:04:37 (CPU time = 02:04:35.5) ] tree PAUP_1 = [&R] (((((((GM,MT),LJ),AGI),ST),(OGI,OGI)),((PGI,PGI),((GM,MT),PGI))),(((OGI,OGI),OGI),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:54:56 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28114.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23152 C=0.21971 G=0.27062 T=0.27815 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 220 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 3053.59259 > Number of trees retained = 1 > Time used = 15 sec (CPU time = 14.97 sec) ] tree PAUP_1 = [&R] ((((GM,GM),LJ),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:55:22 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28261.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30892 C=0.19364 G=0.23611 T=0.26133 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 323 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 5035.37991 > Number of trees retained = 1 > Time used = 26 sec (CPU time = 25.95 sec) ] tree PAUP_1 = [&R] ((((GM,MT),ST),AGI),(OGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:55:23 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28336.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27554 C=0.20715 G=0.22520 T=0.29210 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 194 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 4952.06236 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.76 sec) ] tree PAUP_1 = [&R] ((MT,ST),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 21:00:16 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl28418.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28601 C=0.20677 G=0.24501 T=0.26221 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 362 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 290 > Score of best tree(s) found = 4594.71882 > Number of trees retained = 1 > Time used = 00:10:01 (CPU time = 00:10:01.1) ] tree PAUP_1 = [&R] ((((AGI,AGI),AGI),AGI),((((GM,GM),MT),ST),(OGI,OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:56:32 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28588.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22879 C=0.27000 G=0.27096 T=0.23025 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 319 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 68 > Score of best tree(s) found = 4268.18029 > Number of trees retained = 1 > Time used = 00:01:08 (CPU time = 00:01:07.5) ] tree PAUP_1 = [&R] ((((GM,GM),LJ),(ST,MT)),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:56:36 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28756.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31202 C=0.17916 G=0.23579 T=0.27304 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 213 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 3433.80387 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.46 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:19 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28764.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27533 C=0.20181 G=0.23796 T=0.28490 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 400 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 130 > Score of best tree(s) found = 4864.53312 > Number of trees retained = 1 > Time used = 00:02:42 (CPU time = 00:02:41.6) ] tree PAUP_1 = [&R] ((((GM,(GM,MT)),MT),PGI),((ST,ST),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:33 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl28765.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30183 C=0.22350 G=0.20701 T=0.26767 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 198 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 2364.91936 > Number of trees retained = 1 > Time used = 14 sec (CPU time = 13.28 sec) ] tree PAUP_1 = [&R] ((AGI,AGI),(ST,((GM,GM),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 16:54:17 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl28854.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27463 C=0.23103 G=0.22612 T=0.26823 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 551 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 487 > Score of best tree(s) found = 7898.04112 > Number of trees retained = 1 > Time used = 00:37:45 (CPU time = 00:37:45.3) ] tree PAUP_1 = [&R] (((AGI,AGI),((ST,ST),ST)),(((((LJ,MT),GM),GM),LJ),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 17:22:16 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl28942.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22351 C=0.24678 G=0.25579 T=0.27392 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 515 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 392 > Score of best tree(s) found = 6791.11715 > Number of trees retained = 1 > Time used = 00:27:55 (CPU time = 00:27:54.5) ] tree PAUP_1 = [&R] ((((AGI,AGI),AGI),(((GM,GM),LJ),MT)),(((ST,ST),ST),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:37 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29095.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29551 C=0.21739 G=0.22340 T=0.26370 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 171 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 14 > Score of best tree(s) found = 2173.49633 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.02 sec) ] tree PAUP_1 = [&R] (((LJ,MT),GM),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:38 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29136.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.32867 C=0.19059 G=0.21587 T=0.26488 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 111 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2300.82765 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:38 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29160.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31857 C=0.19187 G=0.22963 T=0.25992 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 151 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3688.37771 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.49 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:39 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29208.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27379 C=0.20612 G=0.24943 T=0.27066 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 170 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3 > Score of best tree(s) found = 3850.32938 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.70 sec) ] tree PAUP_1 = [&R] (((GM,MT),LJ),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:40 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29359.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29479 C=0.20438 G=0.23854 T=0.26228 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 132 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3312.60608 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.40 sec) ] tree PAUP_1 = [&R] (((GM,ST),OGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:40 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29390.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30605 C=0.19517 G=0.22875 T=0.27002 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 96 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2057.05290 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.38 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:44 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29493.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26467 C=0.18352 G=0.24195 T=0.30986 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 170 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2843.19867 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.94 sec) ] tree PAUP_1 = [&R] (((GM,MT),(GM,MT)),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29540.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30543 C=0.19844 G=0.22079 T=0.27534 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 317 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 8646.14007 > Number of trees retained = 1 > Time used = 7 sec (CPU time = 6.15 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,(MT,MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 07:59:52 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29562.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28592 C=0.20000 G=0.26291 T=0.25117 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 118 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1779.31887 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.40 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),GM):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:01:02 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl29684.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25823 C=0.25343 G=0.21611 T=0.27223 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 455 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 6683.29017 > Number of trees retained = 1 > Time used = 00:01:09 (CPU time = 00:01:08.9) ] tree PAUP_1 = [&R] (((AGI,AGI),ST),((GM,MT),(GM,GM))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:01:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl30176.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29745 C=0.18611 G=0.25627 T=0.26018 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 239 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 72 > Score of best tree(s) found = 2805.78031 > Number of trees retained = 1 > Time used = 48 sec (CPU time = 48.03 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),AGI),(((GM,GM),MT),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:01:58 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl30199.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28927 C=0.20148 G=0.24000 T=0.26924 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 338 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 9025.47751 > Number of trees retained = 1 > Time used = 7 sec (CPU time = 7.31 sec) ] tree PAUP_1 = [&R] (((OGI,OGI),(GM,GM)),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:02:03 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl3024.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28208 C=0.20400 G=0.23991 T=0.27401 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 178 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 3181.06479 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.88 sec) ] tree PAUP_1 = [&R] (((LJ,MT),GM),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:02:15 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl30423.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31788 C=0.21061 G=0.20939 T=0.26212 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 212 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30 > Score of best tree(s) found = 2501.50927 > Number of trees retained = 1 > Time used = 12 sec (CPU time = 12.40 sec) ] tree PAUP_1 = [&R] (((GM,MT),(GM,MT)),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:02:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl30426.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27465 C=0.19961 G=0.25379 T=0.27195 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 153 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 4625.01513 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.51 sec) ] tree PAUP_1 = [&R] (((GM,GM),MT),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:03:06 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl30562.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27838 C=0.21258 G=0.23114 T=0.27790 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 186 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 76 > Score of best tree(s) found = 2481.48390 > Number of trees retained = 1 > Time used = 49 sec (CPU time = 49.12 sec) ] tree PAUP_1 = [&R] (((((LJ,MT),GM),GM),AGI),(ST,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 13:56:43 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl30715.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27878 C=0.22257 G=0.25371 T=0.24494 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 462 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 2845 > Score of best tree(s) found = 7465.20611 > Number of trees retained = 1 > Time used = 06:00:03 (CPU time = 05:59:46.7) ] tree PAUP_1 = [&R] ((((((OGI,OGI),(OGI,OGI)),OGI),(((((GM,GM),GM),LJ),(MT,MT)),((GM,GM),(MT,MT)))),(((AGI,AGI),AGI),(ST,ST))),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:03:06 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl30907.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27238 C=0.19536 G=0.22520 T=0.30706 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 125 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2734.43949 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.41 sec) ] tree PAUP_1 = [&R] (((MT,MT),GM),LJ):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:37:21 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl30990.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24938 C=0.24616 G=0.26430 T=0.24016 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 282 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 758 > Score of best tree(s) found = 3945.48158 > Number of trees retained = 1 > Time used = 00:34:12 (CPU time = 00:34:11.6) ] tree PAUP_1 = [&R] (((((OGI,OGI),(OGI,OGI)),AGI),(ST,ST)),((((GM,GM),(GM,MT)),LJ),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:03:07 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl31214.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27450 C=0.22886 G=0.20311 T=0.29353 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 136 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3 > Score of best tree(s) found = 3584.72612 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.59 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 10:36:29 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl31311.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25378 C=0.24868 G=0.22850 T=0.26904 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 617 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 994 > Score of best tree(s) found = 9612.04414 > Number of trees retained = 1 > Time used = 01:59:00 (CPU time = 01:58:58.6) ] tree PAUP_1 = [&R] (((GM,MT),((AGI,AGI),(OGI,OGI))),((((ST,ST),AGI),(((GM,LJ),MT),MT)),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 13:05:56 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl31390.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25871 C=0.22192 G=0.25331 T=0.26607 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 570 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1217 > Score of best tree(s) found = 9355.96503 > Number of trees retained = 1 > Time used = 02:29:21 (CPU time = 02:29:08.5) ] tree PAUP_1 = [&R] ((((GM,MT),(((AGI,AGI),ST),((GM,(LJ,MT)),(ST,ST)))),((OGI,OGI),OGI)),((PGI,PGI),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:23:38 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl31476.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27620 C=0.21785 G=0.25459 T=0.25136 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 440 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 290 > Score of best tree(s) found = 5656.97767 > Number of trees retained = 1 > Time used = 00:20:23 (CPU time = 00:20:22.0) ] tree PAUP_1 = [&R] (((AGI,(MT,(GM,MT))),ST),((PGI,PGI),((OGI,OGI),OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:26:58 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl31571.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27971 C=0.21317 G=0.25618 T=0.25094 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 588 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1595 > Score of best tree(s) found = 9374.46211 > Number of trees retained = 1 > Time used = 03:03:14 (CPU time = 03:03:10.9) ] tree PAUP_1 = [&R] ((((AGI,AGI),AGI),(AGI,AGI)),((((((GM,(GM,GM)),LJ),MT),PGI),(GM,MT)),(ST,ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:03:07 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl31617.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30225 C=0.15090 G=0.26486 T=0.28198 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 96 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1600.69022 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.34 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:04:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl31654.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24091 C=0.21107 G=0.26985 T=0.27817 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 241 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 114 > Score of best tree(s) found = 2977.92449 > Number of trees retained = 1 > Time used = 00:01:09 (CPU time = 00:01:08.4) ] tree PAUP_1 = [&R] (((GM,GM),(LJ,MT)),((GM,GM),(LJ,MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:04:23 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl31846.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28496 C=0.19905 G=0.23673 T=0.27926 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 328 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 5756.65336 > Number of trees retained = 1 > Time used = 7 sec (CPU time = 6.58 sec) ] tree PAUP_1 = [&R] (((GM,MT),(AGI,ST)),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:04:46 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl32082.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29537 C=0.21241 G=0.23298 T=0.25924 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 260 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 4034.00637 > Number of trees retained = 1 > Time used = 23 sec (CPU time = 22.31 sec) ] tree PAUP_1 = [&R] ((MT,ST),(OGI,((AGI,AGI),AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:05:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl32194.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31354 C=0.20667 G=0.20950 T=0.27029 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 167 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 2149.47648 > Number of trees retained = 1 > Time used = 14 sec (CPU time = 13.29 sec) ] tree PAUP_1 = [&R] (((ST,ST),ST),(MT,(GM,GM))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:05:47 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl32231.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26758 C=0.23955 G=0.22299 T=0.26988 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 232 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 76 > Score of best tree(s) found = 2688.00484 > Number of trees retained = 1 > Time used = 47 sec (CPU time = 46.53 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),(((GM,GM),LJ),MT)),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:05:52 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl3241.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27886 C=0.21695 G=0.25372 T=0.25047 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 220 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 13 > Score of best tree(s) found = 3342.10246 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.17 sec) ] tree PAUP_1 = [&R] ((GM,(LJ,MT)),(ST,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 13:15:05 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl32561.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30853 C=0.22403 G=0.25211 T=0.21533 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 340 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1613 > Score of best tree(s) found = 5458.60364 > Number of trees retained = 1 > Time used = 01:48:03 (CPU time = 01:48:01.7) ] tree PAUP_1 = [&R] (((OGI,OGI),((PGI,PGI),PGI)),(((AGI,AGI),AGI),((((((GM,GM),GM),LJ),(MT,MT)),LJ),(ST,ST)))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:07:08 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl32597.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26019 C=0.20439 G=0.24299 T=0.29243 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 412 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 5051.74666 > Number of trees retained = 1 > Time used = 00:01:15 (CPU time = 00:01:15.3) ] tree PAUP_1 = [&R] ((((GM,GM),MT),(AGI,AGI)),(PGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:07:12 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl32977.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24710 C=0.22681 G=0.20290 T=0.32319 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 166 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2140.70556 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.40 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:48:06 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl3307.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28446 C=0.19868 G=0.24494 T=0.27192 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 588 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 391 > Score of best tree(s) found = 7806.38185 > Number of trees retained = 1 > Time used = 00:33:30 (CPU time = 00:33:29.1) ] tree PAUP_1 = [&R] (((GM,MT),((OGI,OGI),OGI)),(((AGI,AGI),(ST,ST)),(PGI,GM))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:10:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl33346.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27383 C=0.19994 G=0.23143 T=0.29480 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 525 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 114 > Score of best tree(s) found = 7765.09925 > Number of trees retained = 1 > Time used = 00:02:47 (CPU time = 00:02:47.3) ] tree PAUP_1 = [&R] ((((AGI,AGI),ST),((LJ,MT),GM)),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 08:55:05 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl33795.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26554 C=0.25115 G=0.28545 T=0.19786 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 248 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 275 > Score of best tree(s) found = 3211.24520 > Number of trees retained = 1 > Time used = 00:06:58 (CPU time = 00:06:57.0) ] tree PAUP_1 = [&R] ((((MT,MT),(GM,GM)),LJ),((OGI,OGI),((AGI,AGI),AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:10:01 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl34053.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25214 C=0.22741 G=0.23779 T=0.28266 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 119 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 4 > Score of best tree(s) found = 2506.07171 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.69 sec) ] tree PAUP_1 = [&R] (((LJ,GM),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:10:56 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl34165.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29722 C=0.17060 G=0.26280 T=0.26939 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 276 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 3192.95433 > Number of trees retained = 1 > Time used = 55 sec (CPU time = 54.36 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),((GM,MT),ST)),(GM,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 09:38:18 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl34326.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27514 C=0.22831 G=0.21948 T=0.27706 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 641 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 466 > Score of best tree(s) found = 8282.07528 > Number of trees retained = 1 > Time used = 00:43:08 (CPU time = 00:43:07.3) ] tree PAUP_1 = [&R] ((((AGI,AGI),(GM,ST)),((LJ,(MT,GM)),(AGI,(ST,ST)))),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:10:57 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl34400.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26060 C=0.19251 G=0.23584 T=0.31105 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 121 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2450.34099 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.37 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:12:14 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl34472.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24501 C=0.25148 G=0.24386 T=0.25964 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 530 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 10473.06841 > Number of trees retained = 1 > Time used = 00:01:16 (CPU time = 00:01:15.6) ] tree PAUP_1 = [&R] ((OGI,ST),((AGI,AGI),((LJ,MT),GM))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 10:18:19 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl34566.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26007 C=0.25061 G=0.28672 T=0.20261 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 300 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2125 > Score of best tree(s) found = 4290.88095 > Number of trees retained = 1 > Time used = 02:03:30 (CPU time = 02:03:27.9) ] tree PAUP_1 = [&R] (((((GM,(OGI,OGI)),GM),LJ),((ST,ST),ST)),(((AGI,AGI),AGI),((MT,((PGI,PGI),PGI)),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:14:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl34705.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29821 C=0.17813 G=0.26712 T=0.25654 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 619 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 71 > Score of best tree(s) found = 8590.44189 > Number of trees retained = 1 > Time used = 00:01:45 (CPU time = 00:01:45.3) ] tree PAUP_1 = [&R] ((((GM,GM),(ST,ST)),AGI),(AGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:16:38 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl35136.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30049 C=0.19080 G=0.24952 T=0.25920 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 547 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 649 > Score of best tree(s) found = 6481.56796 > Number of trees retained = 1 > Time used = 00:58:13 (CPU time = 00:58:12.0) ] tree PAUP_1 = [&R] ((((AGI,AGI),AGI),((MT,MT),GM)),(((MT,GM),((LJ,MT),GM)),(AGI,AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:19:10 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl35144.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26544 C=0.22582 G=0.26177 T=0.24698 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 508 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 172 > Score of best tree(s) found = 6256.15124 > Number of trees retained = 1 > Time used = 00:05:09 (CPU time = 00:05:08.8) ] tree PAUP_1 = [&R] (((OGI,PGI),((GM,LJ),MT)),((ST,ST),(AGI,AGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 13:19:01 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl35208.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26450 C=0.22217 G=0.26843 T=0.24490 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 477 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1184 > Score of best tree(s) found = 7037.53697 > Number of trees retained = 1 > Time used = 02:02:17 (CPU time = 02:02:15.1) ] tree PAUP_1 = [&R] ((((GM,LJ),GM),(((ST,(ST,ST)),(GM,(LJ,MT))),((AGI,AGI),(AGI,AGI)))),((OGI,OGI),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:19:54 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl35380.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28842 C=0.20479 G=0.23999 T=0.26680 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 564 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 8842.59933 > Number of trees retained = 1 > Time used = 43 sec (CPU time = 42.28 sec) ] tree PAUP_1 = [&R] (((GM,MT),((AGI,AGI),AGI)),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:19:59 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl35492.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31421 C=0.20310 G=0.23191 T=0.25079 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 172 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 15 > Score of best tree(s) found = 2793.52819 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.39 sec) ] tree PAUP_1 = [&R] (((ST,ST),ST),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:10:11 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl36000.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27376 C=0.22799 G=0.25188 T=0.24636 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 355 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1749 > Score of best tree(s) found = 5400.52510 > Number of trees retained = 1 > Time used = 02:16:39 (CPU time = 02:16:37.4) ] tree PAUP_1 = [&R] ((((LJ,ST),((((GM,GM),(LJ,MT)),MT),MT)),((((OGI,(OGI,OGI)),OGI),OGI),PGI)),((AGI,AGI),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:32:17 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl36027.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29146 C=0.20016 G=0.23874 T=0.26964 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 675 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 275 > Score of best tree(s) found = 9308.76783 > Number of trees retained = 1 > Time used = 00:22:02 (CPU time = 00:22:01.1) ] tree PAUP_1 = [&R] ((AGI,(((LJ,MT),GM),((AGI,AGI),(ST,GM)))),(ST,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:19:59 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl36078.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28990 C=0.18411 G=0.23831 T=0.28768 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 100 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1990.30939 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 14:28:13 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl36336.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29403 C=0.18875 G=0.25563 T=0.26158 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 382 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2057 > Score of best tree(s) found = 5048.61521 > Number of trees retained = 1 > Time used = 02:55:51 (CPU time = 02:55:49.1) ] tree PAUP_1 = [&R] (((GM,LJ),((((((ST,ST),ST),ST),ST),AGI),((GM,((GM,GM),((MT,MT),LJ))),LJ))),((PGI,PGI),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:21:04 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl36370.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27155 C=0.19918 G=0.24330 T=0.28596 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 327 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 4600.39691 > Number of trees retained = 1 > Time used = 00:01:04 (CPU time = 00:01:03.8) ] tree PAUP_1 = [&R] (((GM,MT),((AGI,AGI),OGI)),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:21:04 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl36751.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.32760 C=0.16242 G=0.24246 T=0.26752 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 146 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3632.09458 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.47 sec) ] tree PAUP_1 = [&R] (((GM,LJ),ST),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:22:51 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl36785.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22096 C=0.50673 G=0.04491 T=0.22740 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 307 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 139 > Score of best tree(s) found = 3798.46455 > Number of trees retained = 1 > Time used = 00:01:46 (CPU time = 00:01:46.1) ] tree PAUP_1 = [&R] (((GM,MT),(ST,(((PGI,PGI),PGI),PGI))),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:22:52 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl36934.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.34057 C=0.18257 G=0.23683 T=0.24003 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 106 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2043.25117 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.34 sec) ] tree PAUP_1 = [&R] ((LJ,(GM,GM)),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:23:11 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37061.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24483 C=0.23901 G=0.24698 T=0.26918 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 300 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 4477.01634 > Number of trees retained = 1 > Time used = 18 sec (CPU time = 18.51 sec) ] tree PAUP_1 = [&R] (((LJ,MT),GM),((ST,ST),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:24:07 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37086.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.32563 C=0.18197 G=0.24152 T=0.25088 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 278 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 80 > Score of best tree(s) found = 3194.27165 > Number of trees retained = 1 > Time used = 55 sec (CPU time = 55.74 sec) ] tree PAUP_1 = [&R] ((AGI,(LJ,(MT,(GM,GM)))),(ST,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 09:56:15 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl37110.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28711 C=0.19279 G=0.25207 T=0.26804 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 378 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1406 > Score of best tree(s) found = 4257.48424 > Number of trees retained = 3 > Time used = 01:02:24 (CPU time = 01:02:22.7) ] tree PAUP_1 = [&R] ((((GM,((GM,MT),LJ)),MT),AGI),(ST,((OGI,(OGI,OGI)),OGI))):0.3333; tree PAUP_2 = [&R] ((((GM,((GM,MT),LJ)),MT),AGI),(ST,(((OGI,OGI),OGI),OGI))):0.3333; tree PAUP_3 = [&R] ((((GM,((GM,MT),LJ)),MT),AGI),(ST,(((OGI,OGI),OGI),OGI))):0.3333; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 10:20:38 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl37178.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29086 C=0.21486 G=0.25448 T=0.23980 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 593 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 326 > Score of best tree(s) found = 7197.02940 > Number of trees retained = 1 > Time used = 00:24:19 (CPU time = 00:24:18.1) ] tree PAUP_1 = [&R] ((((((GM,(GM,LJ)),MT),ST),AGI),AGI),((OGI,OGI),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:29:53 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37251.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28834 C=0.19056 G=0.24945 T=0.27165 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 535 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 172 > Score of best tree(s) found = 6944.57585 > Number of trees retained = 1 > Time used = 00:05:44 (CPU time = 00:05:43.6) ] tree PAUP_1 = [&R] ((((AGI,AGI),(MT,MT)),(ST,ST)),((OGI,OGI),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:29:56 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37468.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26407 C=0.19618 G=0.20164 T=0.33811 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 184 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2233.74882 > Number of trees retained = 1 > Time used = 3 sec (CPU time = 3.51 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),(MT,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:08:33 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl37605.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24967 C=0.24603 G=0.23341 T=0.27088 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 397 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1283 > Score of best tree(s) found = 4237.91221 > Number of trees retained = 3 > Time used = 00:47:49 (CPU time = 00:47:47.4) ] tree PAUP_1 = [&R] ((((AGI,AGI),AGI),(ST,ST)),(MT,(((GM,(GM,GM)),GM),LJ))):0.3333; tree PAUP_2 = [&R] ((((AGI,AGI),AGI),(ST,ST)),(MT,(((GM,(GM,GM)),GM),LJ))):0.3333; tree PAUP_3 = [&R] (((AGI,(AGI,AGI)),(ST,ST)),(MT,(((GM,(GM,GM)),GM),LJ))):0.3333; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:30:03 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37653.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27917 C=0.22390 G=0.26090 T=0.23603 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 301 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4710.08447 > Number of trees retained = 1 > Time used = 6 sec (CPU time = 6.10 sec) ] tree PAUP_1 = [&R] ((((GM,GM),LJ),AGI),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:35:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37747.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26561 C=0.20267 G=0.25843 T=0.27330 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 387 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 267 > Score of best tree(s) found = 5165.48236 > Number of trees retained = 1 > Time used = 00:05:12 (CPU time = 00:05:11.9) ] tree PAUP_1 = [&R] ((((GM,GM),GM),((((MT,MT),MT),LJ),GM)),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:35:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37814.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28715 C=0.17651 G=0.24382 T=0.29252 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 144 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2292.46299 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.58 sec) ] tree PAUP_1 = [&R] ((ST,ST),(GM,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:35:18 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37845.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28867 C=0.18248 G=0.26277 T=0.26608 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 166 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 4538.73400 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.53 sec) ] tree PAUP_1 = [&R] (((GM,MT),GM),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:36:28 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37881.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24115 C=0.22605 G=0.27135 T=0.26144 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 260 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 99 > Score of best tree(s) found = 3166.90726 > Number of trees retained = 1 > Time used = 00:01:09 (CPU time = 00:01:09.8) ] tree PAUP_1 = [&R] ((((OGI,GM),ST),(GM,GM)),(GM,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:37:09 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37892.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26845 C=0.20338 G=0.26246 T=0.26572 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 574 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 8450.74409 > Number of trees retained = 1 > Time used = 40 sec (CPU time = 39.89 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),OGI),((GM,LJ),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:37:10 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl37926.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28685 C=0.19566 G=0.27471 T=0.24277 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 279 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 9911.96256 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.85 sec) ] tree PAUP_1 = [&R] ((OGI,OGI),(PGI,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:37:14 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl3799.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26510 C=0.21138 G=0.24103 T=0.28248 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 196 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4157.69252 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.53 sec) ] tree PAUP_1 = [&R] ((((GM,LJ),LJ),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:37:15 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38074.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27922 C=0.22566 G=0.21682 T=0.27830 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 157 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 4152.35273 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.53 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:37:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38106.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31153 C=0.18641 G=0.24107 T=0.26098 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 125 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 2013.58004 > Number of trees retained = 1 > Time used = 2 sec (CPU time = 2.39 sec) ] tree PAUP_1 = [&R] (((GM,GM),(LJ,MT)),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:37:36 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl3812.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27993 C=0.19280 G=0.24874 T=0.27853 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 175 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 47 > Score of best tree(s) found = 2321.07491 > Number of trees retained = 1 > Time used = 19 sec (CPU time = 18.56 sec) ] tree PAUP_1 = [&R] (((GM,(MT,PGI)),LJ),(ST,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 01:32:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38197.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28282 C=0.24396 G=0.24543 T=0.22779 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 1380 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 273 > Score of best tree(s) found = 36346.32598 > Number of trees retained = 1 > Time used = 06:01:06 (CPU time = 06:00:32.1) ] tree PAUP_1 = [&R] ((((((AGI,AGI),(AGI,AGI)),(AGI,(((AGI,AGI),AGI),AGI))),(((ST,ST),ST),((((((((AGI,AGI),(AGI,AGI)),((AGI,(MT,MT)),(ST,(ST,ST)))),((GM,GM),(((MT,MT),MT),MT))),(((((PGI,PGI),PGI),PGI),((((PGI,PGI),PGI),PGI),((PGI,(PGI,PGI)),PGI))),((((((PGI,PGI),PGI),(PGI,PGI)),(PGI,PGI)),(((PGI,(PGI,PGI)),PGI),PGI)),PGI))),((MT,MT),LJ)),((GM,GM),(LJ,LJ))),(((((GM,(GM,GM)),LJ),(MT,(MT,MT))),MT),PGI)))),((((GM,GM),(GM,(GM,GM))),LJ),GM)),((((((OGI,OGI),((OGI,OGI),OGI)),OGI),((OGI,OGI),(AGI,OGI))),((((PGI,PGI),PGI),PGI),PGI)),((GM,GM),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:39:50 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38260.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27388 C=0.20950 G=0.25734 T=0.25928 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 339 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 136 > Score of best tree(s) found = 3880.61757 > Number of trees retained = 1 > Time used = 00:02:13 (CPU time = 00:02:13.1) ] tree PAUP_1 = [&R] ((((GM,(GM,(LJ,MT))),LJ),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:42:13 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38315.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27522 C=0.21700 G=0.22722 T=0.28056 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 365 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 119 > Score of best tree(s) found = 5413.43993 > Number of trees retained = 1 > Time used = 00:02:22 (CPU time = 00:02:21.7) ] tree PAUP_1 = [&R] (((AGI,AGI),(GM,(LJ,MT))),((PGI,PGI),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:42:13 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38342.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23306 C=0.19285 G=0.24932 T=0.32478 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 89 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = 3468.62308 > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 3588.80472 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] (((AGI,LJ),OGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 10:06:05 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl38403.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28094 C=0.19666 G=0.27324 T=0.24917 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 632 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 628 > Score of best tree(s) found = 9527.67443 > Number of trees retained = 1 > Time used = 01:12:07 (CPU time = 01:12:06.5) ] tree PAUP_1 = [&R] ((((AGI,AGI),(ST,ST)),(((GM,LJ),(MT,MT)),GM)),((PGI,PGI),(OGI,OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:42:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38418.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27346 C=0.18937 G=0.26505 T=0.27212 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 196 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 21 > Score of best tree(s) found = 2362.92171 > Number of trees retained = 1 > Time used = 7 sec (CPU time = 6.79 sec) ] tree PAUP_1 = [&R] (((GM,MT),(PGI,ST)),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:43:01 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38861.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27611 C=0.17471 G=0.24852 T=0.30066 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 281 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 3796.50740 > Number of trees retained = 1 > Time used = 41 sec (CPU time = 40.31 sec) ] tree PAUP_1 = [&R] (((GM,MT),ST),((AGI,AGI),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:43:03 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38937.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29322 C=0.18999 G=0.22108 T=0.29571 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 130 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 1991.28198 > Number of trees retained = 1 > Time used = 2 sec (CPU time = 2.23 sec) ] tree PAUP_1 = [&R] ((GM,MT),((LJ,MT),GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:43:04 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl38960.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28124 C=0.21669 G=0.23745 T=0.26463 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 109 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1848.68026 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.41 sec) ] tree PAUP_1 = [&R] ((LJ,MT),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:43:28 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl39175.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27910 C=0.21265 G=0.21859 T=0.28966 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 379 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30 > Score of best tree(s) found = 4919.65606 > Number of trees retained = 1 > Time used = 23 sec (CPU time = 23.27 sec) ] tree PAUP_1 = [&R] (((GM,MT),(ST,ST)),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:26 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl39535.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25629 C=0.21345 G=0.24752 T=0.28274 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 452 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 130 > Score of best tree(s) found = 5460.01315 > Number of trees retained = 1 > Time used = 00:02:56 (CPU time = 00:02:56.0) ] tree PAUP_1 = [&R] (((((GM,(LJ,MT)),GM),AGI),(ST,ST)),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:26 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl39559.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31678 C=0.15760 G=0.25256 T=0.27305 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 87 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1824.87437 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.35 sec) ] tree PAUP_1 = [&R] (((LJ,MT),GM),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 10:58:13 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl39646.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30196 C=0.19078 G=0.27247 T=0.23478 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 781 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 418 > Score of best tree(s) found = 11188.87431 > Number of trees retained = 1 > Time used = 00:52:01 (CPU time = 00:52:00.4) ] tree PAUP_1 = [&R] ((((AGI,AGI),AGI),(((OGI,ST),(((GM,GM),GM),MT)),ST)),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:31 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl39850.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28432 C=0.21012 G=0.21675 T=0.28881 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 185 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 3400.48035 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 4.15 sec) ] tree PAUP_1 = [&R] ((GM,(MT,LJ)),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:31 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl40066.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28013 C=0.17978 G=0.26576 T=0.27433 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 111 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2853.17288 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.30 sec) ] tree PAUP_1 = [&R] ((LJ,MT),(GM,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:32 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl40080.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29708 C=0.18067 G=0.24374 T=0.27851 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 101 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 4 > Score of best tree(s) found = 2429.13138 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.65 sec) ] tree PAUP_1 = [&R] (((GM,GM),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 19:58:02 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl40277.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25600 C=0.23323 G=0.26536 T=0.24541 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 770 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 867 > Score of best tree(s) found = 16816.19461 > Number of trees retained = 3 > Time used = 06:00:02 (CPU time = 05:59:46.0) ] tree PAUP_1 = [&R] (((((((ST,ST),(AGI,AGI)),(((MT,MT),LJ),GM)),(OGI,(OGI,OGI))),(((GM,LJ),(GM,(GM,GM))),(MT,MT))),(ST,ST)),((((((ST,ST),MT),AGI),(PGI,PGI)),(((PGI,PGI),PGI),((PGI,PGI),PGI))),AGI)):0.3333; tree PAUP_2 = [&R] (((((((ST,ST),(AGI,AGI)),(((MT,MT),LJ),GM)),(OGI,(OGI,OGI))),(((GM,LJ),(GM,(GM,GM))),(MT,MT))),(ST,ST)),((((((ST,ST),MT),AGI),(PGI,PGI)),(((PGI,PGI),PGI),(PGI,(PGI,PGI)))),AGI)):0.3333; tree PAUP_3 = [&R] (((((((ST,ST),(AGI,AGI)),(((MT,MT),LJ),GM)),(OGI,(OGI,OGI))),(((GM,LJ),(GM,(GM,GM))),(MT,MT))),(ST,ST)),((((((ST,ST),MT),AGI),(PGI,PGI)),(((PGI,PGI),PGI),((PGI,PGI),PGI))),AGI)):0.3333; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:36 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl40325.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30229 C=0.18602 G=0.22551 T=0.28618 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 187 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 4745.61869 > Number of trees retained = 1 > Time used = 4 sec (CPU time = 3.78 sec) ] tree PAUP_1 = [&R] ((((GM,LJ),AGI),OGI),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 12:35:42 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl40637.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25876 C=0.21814 G=0.23365 T=0.28945 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 478 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1176 > Score of best tree(s) found = 6514.00852 > Number of trees retained = 1 > Time used = 01:37:24 (CPU time = 01:37:22.9) ] tree PAUP_1 = [&R] ((GM,(MT,((MT,ST),(GM,LJ)))),((((GM,LJ),(MT,MT)),(((GM,GM),MT),GM)),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:46:37 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl40726.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28722 C=0.18364 G=0.25720 T=0.27194 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 164 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5512.72294 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.61 sec) ] tree PAUP_1 = [&R] ((GM,MT),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 11:40:09 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl40894.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28581 C=0.21799 G=0.19573 T=0.30047 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 672 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 919 > Score of best tree(s) found = 9128.28670 > Number of trees retained = 1 > Time used = 01:36:59 (CPU time = 01:36:58.1) ] tree PAUP_1 = [&R] ((((((GM,GM),MT),(MT,MT)),LJ),GM),(((GM,GM),GM),(((MT,MT),MT),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:47:42 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl40968.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23217 C=0.21029 G=0.21517 T=0.34237 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 168 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 138 > Score of best tree(s) found = 3170.31982 > Number of trees retained = 1 > Time used = 00:01:04 (CPU time = 00:01:04.7) ] tree PAUP_1 = [&R] ((((AGI,((LJ,GM),MT)),ST),OGI),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 12:15:20 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl41618.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23158 C=0.26319 G=0.25350 T=0.25173 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 464 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 525 > Score of best tree(s) found = 5721.93257 > Number of trees retained = 1 > Time used = 00:35:07 (CPU time = 00:35:06.0) ] tree PAUP_1 = [&R] (((AGI,AGI),(((GM,GM),(MT,LJ)),LJ)),(((GM,GM),(MT,MT)),AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 13:17:32 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl41691.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29053 C=0.21392 G=0.21965 T=0.27589 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 387 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 674 > Score of best tree(s) found = 5307.33641 > Number of trees retained = 1 > Time used = 01:02:05 (CPU time = 01:02:04.2) ] tree PAUP_1 = [&R] (((GM,MT),(((AGI,AGI),OGI),ST)),(((PGI,PGI),PGI),(((GM,MT),LJ),ST))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 12:13:50 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl41743.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22377 C=0.31227 G=0.26567 T=0.19829 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 338 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 392 > Score of best tree(s) found = 3824.81111 > Number of trees retained = 1 > Time used = 00:20:34 (CPU time = 00:20:33.5) ] tree PAUP_1 = [&R] (((PGI,PGI),((OGI,OGI),(OGI,OGI))),((((GM,GM),OGI),AGI),GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:47:43 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl41944.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25228 C=0.21630 G=0.27857 T=0.25285 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 207 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5922.63855 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.67 sec) ] tree PAUP_1 = [&R] ((AGI,ST),(OGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:53:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl41987.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27986 C=0.20938 G=0.24378 T=0.26698 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 644 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 130 > Score of best tree(s) found = 8844.51961 > Number of trees retained = 1 > Time used = 00:05:31 (CPU time = 00:05:31.3) ] tree PAUP_1 = [&R] (((OGI,OGI),OGI),((((GM,MT),AGI),ST),PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 14:30:54 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl42004.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.23732 C=0.21671 G=0.23129 T=0.31468 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 672 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 1015 > Score of best tree(s) found = 9639.50800 > Number of trees retained = 1 > Time used = 02:16:55 (CPU time = 02:16:53.6) ] tree PAUP_1 = [&R] (((((GM,(MT,((GM,LJ),MT))),AGI),(AGI,AGI)),ST),(((OGI,OGI),PGI),ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:53:40 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42071.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26995 C=0.21193 G=0.25026 T=0.26786 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 326 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 4887.04423 > Number of trees retained = 1 > Time used = 23 sec (CPU time = 23.28 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),((GM,MT),ST)),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 14:39:30 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl42327.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25179 C=0.22655 G=0.25657 T=0.26508 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 325 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 281 > Score of best tree(s) found = 4033.99143 > Number of trees retained = 1 > Time used = 00:08:35 (CPU time = 00:08:34.7) ] tree PAUP_1 = [&R] ((((AGI,AGI),ST),(GM,(LJ,(MT,MT)))),(GM,(OGI,OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:53:58 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42369.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.22681 C=0.22740 G=0.24059 T=0.30520 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 272 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 30 > Score of best tree(s) found = 3659.41750 > Number of trees retained = 1 > Time used = 18 sec (CPU time = 18.08 sec) ] tree PAUP_1 = [&R] (((AGI,AGI),(LJ,MT)),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:53:59 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42399.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27976 C=0.22718 G=0.24372 T=0.24934 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 124 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2248.41380 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.56 sec) ] tree PAUP_1 = [&R] ((GM,GM),(LJ,MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:54:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42440.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29139 C=0.19344 G=0.25990 T=0.25526 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 186 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5592.39566 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.56 sec) ] tree PAUP_1 = [&R] ((OGI,OGI),(AGI,GM)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 16:29:50 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl42477.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26900 C=0.18711 G=0.25121 T=0.29268 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 445 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 260 > Score of best tree(s) found = 5040.97418 > Number of trees retained = 1 > Time used = 00:16:46 (CPU time = 00:16:45.0) ] tree PAUP_1 = [&R] (((AGI,AGI),((ST,ST),((LJ,GM),MT))),((PGI,PGI),OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:54:00 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42554.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25462 C=0.20658 G=0.24021 T=0.29860 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 110 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1963.11259 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.37 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:00:47 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl42625.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26876 C=0.21827 G=0.24965 T=0.26332 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 699 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 624 > Score of best tree(s) found = 10754.38864 > Number of trees retained = 1 > Time used = 01:30:49 (CPU time = 01:30:47.0) ] tree PAUP_1 = [&R] (((((AGI,AGI),AGI),((GM,MT),(ST,ST))),(GM,MT)),((OGI,OGI),(PGI,PGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:54:53 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42881.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31115 C=0.21943 G=0.25162 T=0.21780 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 210 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 64 > Score of best tree(s) found = 2440.20121 > Number of trees retained = 1 > Time used = 52 sec (CPU time = 51.95 sec) ] tree PAUP_1 = [&R] (((AGI,ST),(OGI,OGI)),((GM,GM),MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:54:54 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl42924.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27621 C=0.21844 G=0.25349 T=0.25187 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 168 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2720.50260 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.82 sec) ] tree PAUP_1 = [&R] (((GM,MT),ST),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:22:15 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl42984.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30820 C=0.21587 G=0.23064 T=0.24529 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 405 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 378 > Score of best tree(s) found = 5218.03710 > Number of trees retained = 1 > Time used = 00:21:25 (CPU time = 00:21:24.8) ] tree PAUP_1 = [&R] ((((((GM,GM),(MT,LJ)),AGI),(ST,ST)),(ST,ST)),(PGI,PGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 17:43:04 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl4338.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27889 C=0.22111 G=0.24582 T=0.25418 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 727 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 652 > Score of best tree(s) found = 10702.08929 > Number of trees retained = 1 > Time used = 01:29:40 (CPU time = 01:29:38.7) ] tree PAUP_1 = [&R] (((((AGI,AGI),AGI),AGI),(((GM,(LJ,MT)),(GM,MT)),(ST,ST))),(OGI,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:54:55 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl43829.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25288 C=0.20160 G=0.25481 T=0.29071 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 146 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2505.71640 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.52 sec) ] tree PAUP_1 = [&R] (((GM,MT),GM),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:19 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl43928.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28671 C=0.19474 G=0.26277 T=0.25577 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 298 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 35 > Score of best tree(s) found = 3611.41485 > Number of trees retained = 1 > Time used = 23 sec (CPU time = 23.53 sec) ] tree PAUP_1 = [&R] ((((GM,LJ),(ST,ST)),GM),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:20 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl44057.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30768 C=0.18916 G=0.22504 T=0.27811 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 184 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 6547.24871 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.77 sec) ] tree PAUP_1 = [&R] (((GM,MT),ST),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:26 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl44157.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.30720 C=0.23295 G=0.19962 T=0.26023 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 121 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 12 > Score of best tree(s) found = 1893.16322 > Number of trees retained = 1 > Time used = 6 sec (CPU time = 5.87 sec) ] tree PAUP_1 = [&R] (((GM,MT),ST),(AGI,AGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:26 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl44339.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26185 C=0.21914 G=0.26655 T=0.25246 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 119 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1923.29345 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.39 sec) ] tree PAUP_1 = [&R] ((GM,GM),(MT,LJ)):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 12:47:02 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl44395.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.19031 C=0.23489 G=0.26425 T=0.31055 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 315 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3003 > Score of best tree(s) found = 5761.13731 > Number of trees retained = 1 > Time used = 04:50:10 (CPU time = 04:50:04.7) ] tree PAUP_1 = [&R] (((GM,(GM,(OGI,OGI))),LJ),(((((((AGI,PGI),AGI),GM),(AGI,((((GM,LJ),GM),MT),LJ))),((ST,ST),ST)),MT),MT)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:27 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl44659.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31387 C=0.19882 G=0.25339 T=0.23392 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 108 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2048.59800 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] (((LJ,MT),GM),GM):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:27 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl44676.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24877 C=0.21071 G=0.26638 T=0.27414 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 100 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 1873.67745 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.33 sec) ] tree PAUP_1 = [&R] (((GM,GM),LJ),MT):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 08:55:46 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl44677.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.28154 C=0.22618 G=0.19567 T=0.29661 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 250 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 34 > Score of best tree(s) found = 3519.22136 > Number of trees retained = 1 > Time used = 19 sec (CPU time = 18.74 sec) ] tree PAUP_1 = [&R] (((GM,MT),((GM,LJ),MT)),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:01:38 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl4479.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27377 C=0.20097 G=0.26662 T=0.25864 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 860 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 130 > Score of best tree(s) found = 12820.47344 > Number of trees retained = 1 > Time used = 00:05:49 (CPU time = 00:05:48.6) ] tree PAUP_1 = [&R] (((OGI,OGI),PGI),(GM,(((AGI,AGI),AGI),MT))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 23:43:22 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl44840.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.29183 C=0.20692 G=0.22626 T=0.27499 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 785 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 1459 > Score of best tree(s) found = 12782.90808 > Number of trees retained = 1 > Time used = 06:00:08 (CPU time = 06:00:02.9) ] tree PAUP_1 = [&R] ((((ST,ST),AGI),(((((AGI,AGI),((GM,GM),MT)),ST),((MT,GM),MT)),(((OGI,OGI),OGI),OGI))),(PGI,(PGI,PGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 23:58:27 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl44862.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24096 C=0.26518 G=0.25631 T=0.23755 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 538 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 279 > Score of best tree(s) found = 6722.91020 > Number of trees retained = 1 > Time used = 00:15:02 (CPU time = 00:15:01.3) ] tree PAUP_1 = [&R] ((((ST,ST),ST),(((GM,MT),GM),((AGI,AGI),AGI))),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:01:39 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl45129.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.31425 C=0.16258 G=0.23483 T=0.28834 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 120 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2285.50520 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 1.15 sec) ] tree PAUP_1 = [&R] (((ST,ST),MT),PGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Sun Mar 26 18:47:21 2006] [! >Data file = /home/mmcmahon/projects/EST/nexfiles/cl45248.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26322 C=0.20864 G=0.25334 T=0.27480 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 429 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > Time limit of 21600 seconds imposed > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search terminated by time limit (while swapping on tree #1) > Total number of rearrangements tried = 1701 > Score of best tree(s) found = 7975.92545 > Number of trees retained = 1 > Time used = 06:00:08 (CPU time = 05:59:52.5) ] tree PAUP_1 = [&R] (((((((GM,MT),GM),LJ),((PGI,PGI),PGI)),(AGI,AGI)),(((((GM,GM),LJ),MT),MT),(AGI,AGI))),(((ST,ST),(ST,ST)),((OGI,OGI),OGI))):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:01:40 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl45273.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.26209 C=0.19297 G=0.25383 T=0.29111 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 121 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 4 > Score of best tree(s) found = 3095.65347 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.74 sec) ] tree PAUP_1 = [&R] (((GM,LJ),MT),ST):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:01:41 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl45403.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25922 C=0.20324 G=0.27462 T=0.26291 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 194 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 3 > Score of best tree(s) found = 5240.45555 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.81 sec) ] tree PAUP_1 = [&R] ((AGI,(ST,MT)),OGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:02:15 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl45411.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.19207 C=0.23304 G=0.24397 T=0.33092 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 242 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 67 > Score of best tree(s) found = 3382.13729 > Number of trees retained = 1 > Time used = 34 sec (CPU time = 33.88 sec) ] tree PAUP_1 = [&R] ((((GM,LJ),(GM,LJ)),MT),(ST,ST)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:02:16 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl46102.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.25753 C=0.19635 G=0.27519 T=0.27093 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 177 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 2950.50279 > Number of trees retained = 1 > Time used = 1 sec (CPU time = 0.53 sec) ] tree PAUP_1 = [&R] ((AGI,ST),(ST,OGI)):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:02:17 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl46104.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.27313 C=0.19740 G=0.24271 T=0.28676 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 204 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-reconnection (TBR) > Steepest descent option not in effect > 'MaxTrees' setting = 10000 (will not be increased) > Zero-length branches not collapsed > 'MulTrees' option in effect > Topological constraints not enforced > Trees are unrooted > >Heuristic search completed > Total number of rearrangements tried = 2 > Score of best tree(s) found = 5160.58814 > Number of trees retained = 1 > Time used = <1 sec (CPU time = 0.62 sec) ] tree PAUP_1 = [&R] (((GM,MT),ST),AGI):1.0000; End; #NEXUS Begin trees; [Treefile saved Fri Mar 24 09:02:44 2006] [! >Data file = /home/mmcmahon/EST/analyses/nexfiles/cl46124.nex >Heuristic search settings: > Optimality criterion = likelihood > Likelihood settings: > Transition/transversion ratio estimated via ML > Assumed nucleotide frequencies (empirical frequencies): > A=0.24078 C=0.23180 G=0.25623 T=0.27119 > Among-site rate variation: > Assumed proportion of invariable sites = none > Distribution of rates at variable sites = gamma (discrete approximation) > Shape parameter (alpha) = estimated > Number of rate categories = 4 > Representation of average rate for each category = mean > These settings correspond to the HKY85+G model > Number of distinct data patterns under this model = 352 > Molecular clock not enforced > Starting branch lengths obtained using Rogers-Swofford approximation method > Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration > Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06 > -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities > Starting tree(s) obtained via neighbor-joining > Branch-swapping algorithm: tree-bisection-re