HYPHY (software)

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 January 2009, approximately 250 peer-reviewed scientific journal articles cite HYPHY.[3]

HYPHY is developed by Sergei Kosakovsky Pond and Art Poon of UC San Diego, Spencer Muse of North Carolina State University and Simon DW Frost of Cambridge University.

Contents

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.[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

The development of HyPhy started in 1997, with the first public release in 2000 and the most recent version as of Jan 2009 being 0.99+ beta, compiled on May 8, 2008.[2]

Software/code availability and license

HYPHY is distributed as freeware with source code released under the GPL. Compiled binaries for Mac OS (9 and X) and Windows are available for download. The source code is available so that users can compile the HyPhy application on *nix 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]

Notes

  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". http://www.hyphy.org. Retrieved 2009-01-22. 
  3. ^ "Search for papers citing the HYPHY publication on Google Scholar". http://scholar.google.com/scholar?hl=en&lr=&cites=7266052658838931059. Retrieved 2009-01-22. 
  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. http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15713735. Retrieved 2009-01-22. 

External links