PHAST and RPHAST: phylogenetic analysis with space/time models
Open accessAbstract
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 t…
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The PHAST method tests a model allowing substitution rates shift in a specified subset of branches against a null model with constant rate for all branches using likelihood ratio.
“The PHAST method (Hubisz et al. 2011) tests a model allowing substitution rates shift in a specified subset of branches against a null model with constant rate for all branches using likelihood ratio.”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Hubisz et al. 2011
Comparative genomics analyses (species-tree inference, comparative annotation, selection detection) require genome alignments.
“Comparative genomics analyses, including species-tree inference7,8, comparative annotation9,10, and selection detection11,12, require genome alignments.”
From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [11]
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- Authors
- Hubisz, M. J., Pollard, K. S., & Siepel, A.
- Affiliations
- Cornell University (US)
- Gladstone Institutes (US)
- University of California, Santa Cruz (US)
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-12-21
- Volume
- 12
- Issue
- 1
- Pages
- 41-51
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- PMC
- PMC3030812
- OpenAlex
- W2146127418
- Cited by
- 490
- References
- 3
- Citations by year
- 2026: 49 · 2025: 55 · 2024: 54 · 2023: 42 · 2022: 48 · 2021: 40 · 2020: 38 · 2019: 37 · 2018: 26 · 2017: 18 · 2016: 18 · 2015: 20 · 2014: 20 · 2013: 12 · 2012: 8
- FWCI
- 3.03
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Briefings in Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM082901)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- PHAST, phylogenetic analysis, comparative genomics, phylogenomics, spatio-temporal modeling, UCSC Genome Browser, phylogenetic tree, genome annotation, R interface
- MeSH terms
- Phylogeny, Software, Information Storage and Retrieval, Genome, Internet, Genomics, Databases, Genetic
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