Data for "Eighty million years of rapid evolution of the primate Y chromosomes"
dataset
posted on 2022-11-16, 05:57 authored by Yang Zhou, Xiaoyu Zhan, Jiazheng Jin, Long Zhou, Juraj Bergman, Xuemei LiXuemei Li, Marjolaine Marie C Rousselle, Meritxell Riera Belles, Lan ZhaoLan Zhao, Miaoquan Fang, Qi Fang, Lukas KudernaLukas Kuderna, Tomas Marques-Bonet, Haruka Kitayama, Takashi Hayakawa, Yong-Gang Yao, Huanming Yang, David N. Cooper, Xiaoguang Qi, Dong-Dong Wu, Mikkel Heide Schierup, Guojie ZhangThis 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.
