Phyx: phylogenetic tools for unix.
CONCLUSIONS
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.


METHODS
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.


BACKGROUND
eebsmith@umich.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
Joseph W
JW
Brown
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
Joseph F
JF
Walker
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
Stephen A
SA
Smith
D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D012984:Software