Introduction

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.

Publications

  1. Phyx: phylogenetic tools for unix.
    Cite this
    Brown JW, Walker JF, Smith SA, 2017-02-01 - Bioinformatics (Oxford, England)

Credits

  1. Joseph W Brown
    Developer

    Department of Ecology & Evolutionary Biology, University of Michigan, United States of America

  2. Joseph F Walker
    Developer

    Department of Ecology & Evolutionary Biology, University of Michigan, United States of America

  3. Stephen A Smith
    Investigator

    Department of Ecology & Evolutionary Biology, University of Michigan, United States of America

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Summary
AccessionBT001549
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByStephen A Smith