Phyx
Computational Tool
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General Information
DescriptionPhylogenetic tools for unix
Homepagehttps://github.com/FePhyFoFum/phyx
Publications
Phyx: phylogenetic tools for unix
Joseph W. Brown; Joseph F. Walker; Stephen A. Smith
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.
DOI: https://doi.org/10.1093/bioinformatics/btx063
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