Data for "Eighty million years of rapid evolution of the primate Y chromosomes"

This folder contains data for "Eighty million years of rapid evolution of the primate Y chromosome" gene_set.zip contains gene annotation (GFF, CDS, PEP, POS.ADD) for the 30 species used in this study XY_location.zip contains the genomic coordinates for PAR, nonPARX and nonPARY (BED format). Species names are in the 4th column. gametolog_alignment.tar.gz contains gametolog alignment (PHY format) used to calculate pairwise dN/dS. S5.tree.zip contains alignment (FASTA format) and constructed phylogeny (NWK format) for each S5 gametologs. Conserved_Segments.100K.inferCARs contains conserved blocks of the X chromosome across species (inferCARs format) XY_SV.zip contains the sequences used in Y reconstruction analysis (FASTA format), and the recontruction results under 30 Kb resolution (30K/) and 50 Kb resolution (50K/) NLGN4XY.sort.prank.best.fas contains alignment of NLGN4X/Y of each primate trait_selection_analysis.zip contains sequence alignment (FASTA format) of each Y-linked genes used for dN/dS calculation in trait selection analysis.