#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