ACD 3/23/04

Files to accompany "Driskell et al."  submitted March 2004

*Sequence data files contain information on all of the sequences we analyzed.
	-Each line of these two files corresponds to a sequence, and there are six tab-delimited 
		fields for each sequence.
	-Field 1 is "fakegi" a unique identifying number assigned to each sequence in a dataset.  
		(Numbers may overlap between datasets).
	-Field 2 is "nucgi" (gbpln) or "accid" (sprot).  These numbers are the identifying numbers in 
		the Genbank and Swiss-Prot databases, respectively.
	-Field 3 is "taxid" and is the NCBI taxonomy id number attached to the sequence.
	-Field 4 is "clustid" and refers to the cluster in which the sequence was parsed by BLASTCLUST 
		with a 60% minimum sequence similarity. (Cluster numbers overlap between datasets).
	-Fields 5 & 6 designate the cluster into which the sequence was placed as "informative/NONinformative" 
		(Field 5).  If a cluster contains sequence from more than three taxa, it was classed as 
		informative.  The last field (6) designates whether the cluster passed our orthology
		test ("single_copy") or not ("mixed") or was "not_tested" (if NONinformative).

*Supermatrix files are the nexus files of the two supermatrices analyzed in this paper.  The data is interleaved
	and grouped by cluster within each nexus file.  
	-each sequence is preceeded by a "name" consisting of the sequence "fakegi" (see above), an underscore, and the taxid 
	-Following the data matrix is a list of taxa and the clusters for which they have data.
	-Following this is a set of TAXSET statements, one for each cluster, listing the taxa which DO NOT 
		have data for that cluster.
	-Lastly there is a set of CHARSET statements, one for each cluster, delineating the characters in the 
		alignment for that cluster.
	-The format line for the green plant supermatrix is constructed so that the assumptions block from 
		a protein parsimony step matrix can be used, although the step matrix is not included in this 
		file. It is, however, also available for download.

*Protein parsimony step matrix is the step matrix that was applied to the green plant supermatrix for parsimony
	analysis.

	
*The two *CLUSTERS.tar.gz files contain all aligned nexus files for all informative clusters.
	-these files are zipped and tarred.  To decompress and detar simultaneously, the command is:
		gzip -dv | tar -xvf
	-Within each set, individual nexus files are labelled as gbpln*.nex (sprot*.nex), where * corresponds 
		to the cluster id number.
	-For the green plants, Clusters 1-3, and 5 were NOT fully aligned, but instead the sequences 
		necessary to build the supermatrix were extracted from the clusters and aligned separately.
		These partial cluster files are labelled as "gbpln*.subset.nex"