Data from: Genomic diversity of the endosymbiotic bacteria of human head lice.

This repository contains data associated with a study of endosymbiotic bacteria. Files beginning with "Phylo" indicate data used in or generated from phylogenetic analysis, beginning with "Cophy" indicated data used in phylogenetic comparisons of the host and endosymbiont, beginning with "Biogeography" indicating distributional data, beginning with "Skyline" indicating data used in generation of a Skyline plot. beginning with "VCFfiles" indicating vcf files resulting from alignment of reads to the genome of Ca. Riesia pediculicola, beginning with "Scaffolds" indicating partial genome assemblies of Ca. Riesia phthiripubis. Example software usage is included for certain phylogenetic software packages. Exact software used and the version of the software is document in the associated publication. VCF files are broken down into files containing structural variants, polymorphic sites, and fixed sites for each sample. File formats include fasta (.fa), newick (.tre), nexus (.nex), phylip (.phy), VCF (.vcf), and comma separated variable (.csv).本仓库收录与内共生细菌（endosymbiotic bacteria）研究相关的数据集。以“Phylo”为前缀的文件代表系统发育分析（phylogenetic analysis）所用或由其生成的数据集；以“Cophy”为前缀的文件代表用于宿主与内共生体系统发育比较分析的数据集；以“Biogeography”为前缀的文件代表分布数据；以“Skyline”为前缀的文件代表用于生成Skyline图（Skyline plot）的数据集；以“VCFfiles”为前缀的文件代表将测序读段（reads）比对至Ca. Riesia pediculicola基因组后得到的VCF文件；以“Scaffolds”为前缀的文件代表Ca. Riesia phthiripubis的部分基因组组装序列。部分系统发育软件包附带了示例使用教程，所用软件的准确名称及版本信息详见相关发表论文。VCF文件按样本分为结构变异（structural variants）、多态位点（polymorphic sites）及固定位点（fixed sites）三类文件。文件格式涵盖fasta（.fa）、newick（.tre）、nexus（.nex）、phylip（.phy）、VCF（.vcf）及逗号分隔值（.csv）格式。