README for Braun and Kimball "Data types and the phylogeny of Neoaves"

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Files:

Concatenated nexus file with charsets for data partitions:
	-- NOTE:	first, second and third codon positions are contiguous in these files;
				the files for individual loci are contiguous sequences

1. Prum-alldata-codonpos-part.nex
2. Prum-exons-codonpos-part.nex
3. Prum-noncoding-part.nex

Files with gene trees:
	-- NOTE:	these are tab-delimited files with the locus number followed by a newick
				string for the tree. This was done to allow information used to generate
				each tree to be traced.  They can be converted into treefiles that can be 
				used as input for ASTRAL as follows:
					awk '{print $2}' NT-gene-trees.txt > NT-gene-trees.tre
					awk '{print $2}' RY-gene-trees.txt > RY-gene-trees.tre
				Alternatively, you can import into a spreadsheet, copy the column of
				newick strings, and paste them into a text file. 

4. NT-gene-trees.txt
5. RY-gene-trees.txt

Other files:

6. Prum-authority-file.txt
	--	List of taxon names used to generate the concatenated files (necessary for the
		simple_concat.pl program available from https://github.com/ebraun68/RYcode)

Separate supplementary files:

7. Supplementary_File_S1.xlsx
	--	MS Excel file with base composition and locus size information.
8. Supplementary_File_S2.tre
	--	Nexus treefile with all trees. Includes taxon block and comments describing each
		tree. Includes the original Prum et al. 2015 trees for comparison.

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Folder:

Annotated-alignments-of-individual-loci 
	--	259 nexus files, one for each locus. Files include a sets block with charsets for
		the three codon positions, for introns, and for UTRs. 

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NOTES:
 --	These files reflect reanalysis of the dataset from Prum et al. 2015. A comprehensive 
 	phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 526, 
 	569-573. doi: 10.1038/nature15697
 --	Gene names for the Prum et al. 2015 loci are available in Reddy_sup_fileS2_PrumLoci
	available from https://datadryad.org/stash/dataset/doi:10.5061/dryad.6536v
 --	The Reddy_sup_fileS2_PrumLoci file was generated using a simple pipeline that produced
 	approximate amounts of coding and non-coding data. The information in the excel file
 	"Base_composition.xlsx" reflects manual data curation so it provides the precise numbers
 	of sites.
