Brown Joseph W, Walker Joseph F, Smith Stephen A
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
Bioinformatics. 2017 Jun 15;33(12):1886-1888. 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.
Supplementary data are available at Bioinformatics online.
系统发育组学数据生成的便捷性极大地增加了即使是常规系统发育研究的计算负担。为解决这一问题，我们推出了phyx：一个用C++编写的程序集合，用于探索、操作、分析和模拟系统发育对象（比对、树和MCMC日志）。该程序以Unix/GNU/Linux命令行工具为模型，各个程序执行单一任务，并在标准I/O流上运行，这些流可以通过管道连接，从而快速轻松地形成复杂的分析管道。由于以流为中心的范式，内存需求被最小化（任何时候内存中通常只有一棵树或一个序列），因此phyx能够高效地处理非常大的数据集。
phyx在符合POSIX标准的操作系统上运行。源代码、安装说明、文档和示例文件可在GNU通用公共许可证下从https://github.com/FePhyFoFum/phyx免费获取。
补充数据可在《生物信息学》在线获取。
