Phyx: phylogenetic tools for unix

被引：211

作者：

Brown, Joseph W. ^{[1
]}

Walker, Joseph F. ^{[1
]}

Smith, Stephen A. ^{[1
]}

机构：

[1] Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA

来源：

BIOINFORMATICS | 2017年 / 33卷 / 12期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/bioinformatics/btx063

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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

引用

页码：1886 / 1888

页数：3

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