| Literature DB >> 31504749 |
Sergei L Kosakovsky Pond1, Art F Y Poon2, Ryan Velazquez1, Steven Weaver1, N Lance Hepler3, Ben Murrell4, Stephen D Shank1, Brittany Rife Magalis1, Dave Bouvier5, Anton Nekrutenko5, Sadie Wisotsky1,6, Stephanie J Spielman1,7, Simon D W Frost8,9, Spencer V Muse6.
Abstract
HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases.Keywords: evolutionary analysis; hypothesis testing; natural selection; software engineering; statistical inference
Mesh：
Year: 2020 PMID： 31504749 PMCID： PMC8204705 DOI： 10.1093/molbev/msz197
Source DB: PubMed Journal: Mol Biol Evol ISSN： 0737-4038 Impact factor: 16.240