For this section, we'll need the tree and phylogenetic information in datasets/ch4/ from the book's data repository, specifically the mammal_tree.nwk and mammal_tree.nexus files, which are Newick and Nexus format trees of a mammal phylogeny (you can see brief descriptions of these file types in this book's Appendix). We'll need beast_mcc.tree, which is a tree file from a run of BEAST, and RAxML_bipartitionsBranchLabels.H3, which is an RAxML output file. Both of these files are taken from the extensive data provided with the treeio package. We'll require the Bioconductor package, treeio, and the ape package.