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

2019; Oxford University Press; Volume: 37; Issue: 1 Linguagem: Inglês

10.1093/molbev/msz197

1537-1719

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

Genetic diversity and population structure

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.