| 词条 | HYPHY (software) |
| 释义 |
| name = HyPhy | developer = Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith. | latest_release_version = June, 2012 | latest_release_date = {{release date|2018|08|07|df=yes}} | programming language = | language = English | genre = Computational phylogenetics | license = | website = {{URL|http://www.hyphy.org/}} }}HYPHY ({{IPAc-en|ˈ|h|aɪ|f|aɪ}} {{respell|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 featuresHYPHY 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. HistoryThe development of HyPhy started in 1997, with the first public release in 2000 and the most recent version as of April 2019 being 2.3.14 .[2] Software/code availability and licenseHYPHY 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] Notes1. ^1 {{cite journal |vauthors=Pond SL, Frost SD, Muse SV |title=HyPhy: hypothesis testing using phylogenies |journal=Bioinformatics |volume=21 |issue=5 |pages=676–9 |date=March 2005 |pmid=15509596 |doi=10.1093/bioinformatics/bti079 |url=}} 2. ^1 {{cite web |url=http://www.hyphy.org |title=HYPHY Package Page |format= |work= |accessdate=2009-01-22}} 3. ^{{cite web |url=https://scholar.google.com/scholar?hl=en&as_sdt=0,39&sciodt=0,39&cites=17874163875017617061&scipsc= |title=Search for papers citing the HYPHY publication on Google Scholar |format= |work= |accessdate=2018-03-23}} 4. ^{{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 |url=http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15713735 |accessdate=2009-01-22}} External links
2 : Computational phylogenetics|Bioinformatics software |
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