HYPHY (software)
| Developer(s) | Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith. |
|---|---|
| Stable release | 2.5.24
/ 17 December 2020 |
| Available in | English |
| Type | Computational phylogenetics |
| Website | www |
HYPHY (/ˈhaɪfaɪ/ 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 December 2020 being 2.5.[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 Temple University on the DataMonkey cluster.[4]
Notes
[edit]- ^ 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.
- ^ a b "HYPHY Package Page". Retrieved 2009-01-22.
- ^ "Search for papers citing the HYPHY publication on Google Scholar". Retrieved 2018-03-23.
- ^ 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.