Phyx: phylogenetic tools for unix

• Published in: Bioinformatics (Oxford, England) Vol. 33; no. 12; pp. 1886 - 1888
• Main Authors: Brown, Joseph W, Walker, Joseph F, Smith, Stephen A
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.06.2017
• Subjects: Applications Notes; Genomics - methods; Phylogeny; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btx063

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. 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. eebsmith@umich.edu. Supplementary data are available at Bioinformatics online.