PHAST and RPHAST: phylogenetic analysis with space/time models
PHAST and RPHAST: phylogenetic analysis with space/time models
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DOI：
10.1093/bib/bbq072
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发表时间：
2011-01-01
影响因子：
9.5
通讯作者：
Siepel, Adam
中科院分区：
文献类型：
--
作者：
Hubisz, Melissa J.;Pollard, Katherine S.;Siepel, Adam
带有时空模型的系统发育分析（PHAST）软件包由一系列命令行程序和用于比较基因组学的支持库组成。PHAST最为人所知的是作为加州大学圣克鲁兹分校（UCSC）基因组浏览器中保守性轨迹背后的引擎。然而，它还包括其他几种用于系统发育建模和功能元件识别的工具，以及用于处理比对、树和基因组注释的实用程序。PHAST自2002年开始开发，现已被下载超过1000次，但到目前为止它仅作为临时（“测试版”）软件发布。在此，我们描述PHAST的首次正式发布版本（v1.0），它具有更高的稳定性、可移植性和文档，以及一些新特性。我们概述了该软件包的组件并详细介绍了近期的改进。此外，我们从R统计计算环境引入了一个到PHAST库的新接口，称为RPHAST，并在一系列示例中说明了它的使用。我们证明RPHAST在涉及大规模系统发育基因组学和复杂统计分析的应用中特别有用。R接口也使非C程序员能够使用PHAST库，并且对于快速构建原型很有用。PHAST v1.0和RPHAST v1.0可根据无限制的BSD风格许可证条款从http://compgen.bscb.cornell.edu/phast下载。RPHAST也可从综合R存档网络（CRAN；http://cran.r - project.org）获取。
The PHylogenetic Analysis with Space/Time models (PHAST) software package consists of a collection of command-line programs and supporting libraries for comparative genomics. PHAST is best known as the engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser. However, it also includes several other tools for phylogenetic modeling and functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations. PHAST has been in development since 2002 and has now been downloaded more than 1000 times, but so far it has been released only as provisional ('beta') software. Here, we describe the first official release (v1.0) of PHAST, with improved stability, portability and documentation and several new features. We outline the components of the package and detail recent improvements. In addition, we introduce a new interface to the PHAST libraries from the R statistical computing environment, called RPHAST, and illustrate its use in a series of vignettes. We demonstrate that RPHAST can be particularly useful in applications involving both large-scale phylogenomics and complex statistical analyses. The R interface also makes the PHAST libraries acccessible to non-C programmers, and is useful for rapid prototyping. PHAST v1.0 and RPHASTv1.0 are available for download at http://compgen.bscb.cornell.edu/phast, under the terms of an unrestrictive BSD-style license. RPHAST can also be obtained from the Comprehensive R Archive Network (CRAN; http://cran.r-project.org).