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PHylogenetic Analysis with Space/Time models PHAST

Online

Allows statistical phylogenetic modeling and functional element identification. PHAST is a collection of programs and supporting libraries for comparative genomics. The software also provides methods for detecting departures from neutrality in rates and patterns of molecular evolution. It is well-suited for analyzing patterns of conservation and acceleration in aligned sequences, and for extracting data from or exporting data to the UCSC Genome Browser and related resources, such as Galaxy.

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PHAST forum

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PHAST versioning

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PHAST classification

PHAST specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://github.com/CshlSiepelLab/phast
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
BSD 3-clause “New” or “Revised” License
Version:
1.4
Maintained:
Yes

Subtools

  • PhastCons

PHAST support

Documentation

Maintainer

  • PHAST <>

Credits

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Publications

Institution(s)

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA

Funding source(s)

Supported by National Science Foundation (grant DBI-0644111); the National Institutes of Health (grant R01-GM082901), a David and Lucile Packard Fellowship for Science and Engineering Past, an Achievement Rewards for College Scientists (ARCS) scholarship and a Graduate Research and Education in Adaptive biotechnology (GREAT) fellowship from the University of California Biotechnology Research and Education Program.

Link to literature

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