I’ve been working with phylogenies in R for a long time. I find the ape and phytools to be the most useful.

The phyloHelpeR is an R package to make a home for some of the functions I use a lot when building and plotting phylogenies in R. At the moment it is home to the following functions:

• tanglePlot() a function to plot two phylogenies based on the same sequences opposite one another so you can see how they differ.
• runRAXML() a function to interact with the command line phylogenetic tree building tool RAxML
• addSNPScale() a function to add a scale to a phylogeny whos branch lengths are scaled to the number of Single Nucleotide Polymorphisms.

As you can see, this R package is a work in progress… As I don’t work on phylogenetics anymore my contributions will be slow but hopefully I’ll still add a few more helpful functions. 👍