HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Pond, Sergei L. Kosakovsky; Poon, Art F. Y.; Velazquez, Ryan; Weaver, Steven; Hepler, N. Lance; Murrell, Ben; Shank, Stephen D.; Magalis, Brittany Rife; Bouvier, Dave; Nekrutenko, Anton; Wisotsky, Sadie R; Spielman, Stephanie J.; Frost, Simon D. W.; Muse, Spencer V.

doi:10.1093/molbev/msz197

articleMolecular Biology and EvolutionAug 25, 2019GREEN OA

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

SLSergei L. Kosakovsky Pond AFArt F. Y. Poon RVRyan Velazquez SWSteven Weaver NLN. Lance Hepler

Temple University · Western University · +7 more institutions

PubMed

Indexed incrossrefdoajpubmed

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…

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Topics & keywords

Topics

Keywords

Biology
Statistical hypothesis testing
Coevolution
Workflow
Range (aeronautics)
Usability
Selection (genetic algorithm)
Sequence (biology)

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