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

Abstract

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. © 2011 The Author. Methods in Ecology and Evolution © 2011 British Ecological Society.