Data and results for the paper:

"Extensive gene tree discordance and hemiplasy shaped
the genomes of North American Columnar cacti"

by

Dario Copetti, Alberto Búrquez, Enriquena Bustamante, Joseph Charboneau, Kevin L. Childs, Luis E. Eguiarte, Seunghee Lee, Tiffany L. Liu, Michelle M. McMahon, Noah K. Whiteman, Rod Wing, Martin F. Wojciechowski, Michael J. Sanderson

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Each of the following are subdirectories

AlignmentReport
	Directory contains an Excel spreadsheet reporting CDS regions and introns kept for each
	gene during data set construction, together with summary statistics.
		Columns:
			Gene name	saguaro gene name
			ML mean		mean of ML bootstrap support for two clades on gene tree
			ML min		minimum
			MP mean		mean of MP bootstrap support for two clade on gene tree
			MP max		minimum
			Ncds		number of cds regions kept
			Nintrons	number of introns kept
			Lcds		total length of cds regions kept
			Lintron		total length of introns kept
			Ltot		total length of cds nucs and intron nucs
			CDSs		IDs of the CDS regions kept (in row order from the annotation file)
			Introns		IDS of the introns kept (using IDs of the flanking CDS regions)
			

AlignmentsByGene
	Contains a subdirectory for each saguaro gene ultimately used in alignments.
	There are found nucleotide and amino acid alignments for each CDS region kept;
	nucleotide alignments for each intron kept. 

	Within each subdirectory is a 'concat' subdirectory, which has the following, for example
		Cgig1_00352.5prime.nex	...	Ignore
		Cgig1_00352.aas.nex	...	Amino acid alignment concatenated across CDSs
		Cgig1_00352.allnucs.nex	...	Nucl alignment concatenated across all introns and CDSs
		Cgig1_00352.exons.nex	...	Nucl alignment concatenated across all CDSs		
		Cgig1_00352.neutral.nex	...	Nucl alignment concatenated across all introns and 3rd positions in codons
	[Note there are equivalent files with other suffixes in phylip and fasta format]

Assemblies
	These are the raw assembly fasta files for the five cacti (v.1.2)

ConcordantDiscordantTrees
	For the two gene confidence sets, this has lists of genes that agree or disagree with the species tree

GeneConfidenceSets
	Lists of genes in the 50-90% gene confidence sets, together with tree files assembled from the
	ML bootstrap trees found in directory 'GeneTreesPaupBootML'

GeneLists
	Lists of all saguaro gene names, and just the genes that were successfully placed into alignments with all 5 cacti.

GeneTreesPaupBootML
	A subdirectory points to each saguaro gene used, within which is the bootstrap ML majority rule
	tree and a paup log file.

NetworksPhyloNet
	Results from PhyloNet's 'InferNetwork_ML' analyses. There are subdirectories for several
	different gene confidence sets and partitions of the alignments.

SaguaroAnnotation
	GFF files containing the final (v.1.3) annotations of the saguaro SGP5 genome assembly.
	Also contains the v.1.3 assembly.

Scripts
	All PERL scripts used to undertake analyses for this paper.

SpeciesTreesBPP
	Contains results of BPP analyses of several gene confidence sets and subalignments.
	Each directory contains the relevant input and output files.

MP-EST
	Contains results of the MP-EST analyses of the gene confidence sets of gene trees