babette: BEAUti 2, BEAST2 and Tracer for R

Abstract

In the field of phylogenetics, BEAST2 is one of the most widely used software tools. It comes with the graphical user interfaces BEAUti 2, DensiTree and Tracer, to create BEAST2 configuration files and to interpret BEAST2's output files. However, when many different alignments or model setups are required, a workflow of graphical user interfaces is cumbersome. Here, we present a free, libre and open-source package, babette: ‘BEAUti 2, BEAST2 and Tracer for R’, for the R programming language. babette creates BEAST2 input files, runs BEAST2 and parses its results, all from an R function call. We describe babette's usage and the novel functionality it provides compared to the original tools and we give some examples. As babette is designed to be of high quality and extendable, we conclude by describing the further development of the package.