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Author Hubisz, Melissa J. ♦ Pollard, Katherine S. ♦ Siepel, Adam
Source PubMed Central
Content type Text
Publisher Oxford University Press
File Format PDF
Date Created 2010-12-22
Copyright Year ©2010
Language English
Difficulty Level Medium
Subject Domain (in DDC) Natural sciences & mathematics ♦ Life sciences; biology ♦ Technology ♦ Medicine & health
Subject Keyword Molecular Biology ♦ Information Systems
Abstract 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 RPHAST v1.0 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).
ISSN 14675463
Age Range above 22 year
Educational Use Research
Interactivity Type Expositive
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2011-01-01
Rights Holder Oxford University Press
e-ISSN 14774054
Journal Briefings in Bioinformatics
Volume Number 12
Issue Number 1
Page Count 11
Starting Page 41
Ending Page 51


Source: PubMed Central