HYPHY ( ) is a free multiplatform (Mac, Windows and UNIX)

computational phylogenetics Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic

software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies". As of March 2018, about 2,000 peer-reviewed scientific journal articles cite HYPHY.

Major features

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. 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

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.

Software/code availability and license

HYPHY is distributed as freeware with source code released under the

MIT License The MIT License is a permissive free software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s. As a permissive license, it puts only very limited restriction on reuse and has, therefore, high license comp ...

. 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 Temple University (Temple or TU) is a public state-related research university in Philadelphia, Pennsylvania. It was founded in 1884 by the Baptist minister Russell Conwell and his congregation Grace Baptist Church of Philadelphia then called Ba ...

on th
DataMonkey
cluster.{{cite journal , vauthors=Pond SL, Frost SD , title=Datamonkey: rapid detection of selective pressure on individual sites of codon alignments , journal=Bioinformatics , volume=21 , issue=10 , pages=2531–3 , date=May 2005 , pmid=15713735 , doi=10.1093/bioinformatics/bti320

Notes

External links

The HYPHY home page

The DataMonkey server, which supports a variety of HYPHY tools (at no cost).

HYPHY/DataMonkey support Phylogenetics software