Reading and writing varied tree formats with ape and treeio
Phylogenetic analysis is a cornerstone of biology and bioinformatics. The programs are diverse and complex, the computations are long-running, and the datasets are often large. Many programs are standalone and many have proprietary input and output formats. This has created a very complex ecosystem that we must navigate when dealing with phylogenetic data, meaning that often the simplest strategy is to use combinations of tools to load, convert, and save the results of analyses in order to be able to use them in different packages. In this recipe, we’ll look at dealing with phylogenetic tree data in R. To date, R support for the wide range of tree formats is restricted, but a few key packages have sufficient standardized objects such that workflows can focus on a few types and conversion to those types is streamlined. We’ll look at using the ape and treeio packages to get tree data into and out of R.
