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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.
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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
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HyPhy includes a versatile suite of methods to detect adaptive evolution at individual amino-acid sites and/or lineages, including generalizations of
Nielsen-Yang
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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.
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A subset of HYPHY methods for detecting adaptive evolution are also made available by the HYPHY team at
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Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith.
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This article is about the phylogenetics software. For the slang term, see
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HYPHY is distributed as freeware with source code released under the
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216:Pond SL, Frost SD, Muse SV (March 2005).
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.