Comparative-genomics-of-horseshoe-bats

ALL the codes used in the study title "Comparative genomics provides insights into chromosomal evolution and immunological adaptation in horseshoe bats"The 'sp20.OrthoFinder.txt.gz' file, generated by the OrthoFinder software, recorded 22,536 gene families. This file was the input for CAFE in gene family analysis.The 'sp20.phy.gz' file recorded the sequence alignments of single-copy orthologs from 20 focal mammals. It was used for the analyses of "Phylogeny construction and divergence time estimation" and "Identification of genes with undergoing both positive selection and rapid evolution".The 'Rhin91.SNP.vcf.gz' file recorded 5,494,189 SNPs for 91 individuals of 10 Rhinolophus species. It was used for constructing a neighbor joining (NJ) tree in TreeBest v1.92, and "Genetic introgression analysis.