Dryad.tgz

You can untar and unzip with tar -xzvf Dryad.tgz. This will create one folder called Dryad. In that folder there are four separate folders. The first contains the 305 species tree and orthologs used to create the tree, seen in figure 3 of the publication. The Next is the Assemblies, these are in both PEP and CDS, they are associated with their keys but those can be changed using the NameKey.txt file. The next folder is FamilyAnalyses, this contains the orthologs, conflict analysis and species tree analyses for the five major families analyzed. The final folder is programs which contains a set of scripts used for the analysis.可通过执行`tar -xzvf Dryad.tgz`命令解压该压缩包，解压完成后将生成一个名为Dryad的文件夹。该文件夹内包含四个独立子文件夹。首个子文件夹内包含305个物种的物种树（species tree）以及用于构建该树的直系同源基因（orthologs），对应论文中的图3内容。第二个子文件夹为组装结果（Assemblies），内含PEP与CDS两种格式的数据；这些数据均配有对应的标识键，可通过NameKey.txt文件修改标识键的对应关系。第三个子文件夹为家族分析（FamilyAnalyses），内含本次分析所涵盖的五个主要类群的直系同源基因、冲突分析以及物种树分析相关数据。最后一个子文件夹为程序工具集（programs），内置本次分析所需的一系列脚本程序。