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. <br> <br> <br>

本文件夹包含论文《灵长类Y染色体八千万年快速演化》的相关实验数据。gene_set.zip内含本研究使用的30个物种的基因注释文件，格式涵盖GFF、CDS、PEP、POS.ADD。XY_location.zip内含假常染色体区域（Pseudoautosomal Region, PAR）、X染色体非假常染色体区域（nonPARX）与Y染色体非假常染色体区域（nonPARY）的基因组坐标信息，文件格式为BED，物种名称位于文件第4列。gametolog_alignment.tar.gz内含用于计算成对dN/dS值的配子同源基因比对文件，格式为PHY。S5.tree.zip内含各S5配子同源基因的序列比对文件（FASTA格式）以及构建完成的系统发育树（NWK格式）。Conserved_Segments.100K.inferCARs内含跨物种的X染色体保守区块，格式为inferCARs。XY_SV.zip内含Y染色体重建分析所用的序列文件（FASTA格式），同时包含30 Kb分辨率（30K/文件夹）与50 Kb分辨率（50K/文件夹）下的重建结果。NLGN4XY.sort.prank.best.fas内含各灵长类NLGN4X/Y基因的序列比对结果。trait_selection_analysis.zip内含用于性状选择分析中dN/dS计算的所有Y连锁基因的序列比对文件，格式为FASTA。