R Bioinformatics Cookbook

How it works...

In Step 1, we make use of very straightforward loading functions from ape—we use the read.tree() and read.nexus() functions, which can read the generic format trees. In Step 2, we repeat this using the specific format functions from treeio for BEAST and RaXML output. Step 3 simply confirms the object types that the function returns; note that ape gives phylo objects, while treeio gives treedata objects. The two are interconverted using as.phylo() and as.treedata() from treeio in Step 4. By converting in this way, we can get input in many formats into downstream analysis in R. Finally, we write the files in Step 5.