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.