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

Overview

Journal Mol Biol Evol

Publisher Oxford University Press

Specialty Biology

Date 2019 Sep 11

PMID 31504749

Citations 251

Authors

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 Wisotsky

Stephanie J Spielman

Simon D W Frost

Spencer V Muse

Affiliations

Soon will be listed here.

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.

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