HYPHY (software)

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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.


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]


  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