HYPHY (software)

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HyPhy
Developer(s) Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith.
Stable release
June, 2012 / 21 June 2012 (2012-06-21)
Available in English
Type Computational phylogenetics
Website www.hyphy.org

HYPHY (/ˈhf/ HY-fy) is a free multiplatform (Mac, Windows and UNIX) Computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses.[1] The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies".[2] As of March 2018, about 2,000 peer-reviewed scientific journal articles cite HYPHY.[3]

Major features[edit]

HYPHY supports analysis of nucleotide, protein and codon sequences, using predefined standard models or user-defined models of evolution. The package supports interaction through a graphical user interface as well as a batch language to set up large and complicated analyses and process the results.[1]

HyPhy includes a versatile suite of methods to detect adaptive evolution at individual amino-acid sites and/or lineages, including generalizations of Nielsen-Yang PAML and Suzuki-Gojobori approaches and many others.

History[edit]

The development of HyPhy started in 1997, with the first public release in 2000 and the most recent version as of July 2012 being 2.12 beta.[2]

Software/code availability and license[edit]

HYPHY is distributed as freeware with source code released under the MIT License. Compiled binaries for Mac OS X and Windows are available for download. The source code is available so that users can compile the HyPhy application on POSIX systems.

A subset of HYPHY methods for detecting adaptive evolution are also made available by the HYPHY team at UC San Diego on the DataMonkey cluster.[4]

Notes[edit]

  1. ^ a b Pond SL, Frost SD, Muse SV (March 2005). "HyPhy: hypothesis testing using phylogenies". Bioinformatics. 21 (5): 676–9. doi:10.1093/bioinformatics/bti079. PMID 15509596. 
  2. ^ a b "HYPHY Package Page". Retrieved 2009-01-22. 
  3. ^ "Search for papers citing the HYPHY publication on Google Scholar". Retrieved 2018-03-23. 
  4. ^ Pond SL, Frost SD (May 2005). "Datamonkey: rapid detection of selective pressure on individual sites of codon alignments". Bioinformatics. 21 (10): 2531–3. doi:10.1093/bioinformatics/bti320. PMID 15713735. Retrieved 2009-01-22. 

External links[edit]

  • [1]: The HYPHY home page
  • [2]: The DataMonkey server, which supports a variety of HYPHY tools (at no cost).
  • [3]: HYPHY/DataMonkey support forums