| HyPhy | |
| Developer: | Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith. |
| Latest Release Version: | 2.5.24 |
| Language: | English |
| Genre: | Computational phylogenetics |
HYPHY 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]
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 December 2020 being 2.5.[2]
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]
The HYPHY home page
The DataMonkey server, which supports a variety of HYPHY tools (at no cost).
HYPHY/DataMonkey support