Phyx: phylogenetic tools for unix

Abstract

Summary: The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx : a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.

Availability and implementation: phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx.

Contact: eebsmith@umich.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Parametric bootstrapping of a diversification process. The primate phylogeny of Springer et al. (2012) was fit to a birth-death model (pxbdfit). To explore the breadth of plausible diversification outcomes the maximum likelihood parameters (b: 0.339487, d: 0.268944) were used to simulate (pxbdsim) 25 000 phylogenies conditioned on either the extant diversity (367, left) or root age (66.7066 Ma, right) of the empirical tree