Rphylip: an R interface for PHYLIP

Abstract

The phylogeny methods software package PHYLIP has long been among the most widely used packages for phylogeny inference and phylogenetic comparative biology. Numerous methods available in PHYLIP, including several new phylogenetic comparative analyses of considerable importance, are not implemented in any other software. Over the past decade, the popularity of the R statistical computing environment for many different types of phylogenetic analyses has soared, particularly in phylogenetic comparative biology. There are now numerous packages and methods developed for the R environment. In this article, we present Rphylip, a new R interface for the PHYLIP package. Functions of Rphylip interface seamlessly with all of the major analysis functions of the PHYLIP package. This new interface will enable the much easier use of PHYLIP programs in an integrated R workflow. In this study, we describe our motivation for developing Rphylip and present an illustration of how functions in the Rphylip package can be used for phylogenetic analysis in R.