phytools: an R package for phylogenetic comparative biology (and other things)

TLDR: A new, multifunctional phylogenetics package, phytools, for the R statistical computing environment is presented, with a focus on phylogenetic tree-building in 2.1.

Abstract: Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.