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Mol Biol Evol. 2019 Aug 27. pii: msz197. doi: 10.1093/molbev/msz197. [Epub ahead of print]

HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.

Author information

1
Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
2
Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
3
10x Genomics, Pleasanton, CA, USA.
4
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
5
Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, USA.
6
Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
7
Rowan University, Glassboro, NJ, USA.
8
Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
9
The Alan Turing Institute, London, United Kingdom.

Abstract

hyphy (HYpothesis testing using PHYlogenies) 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 backwards compatible with previous HyPhy releases.

KEYWORDS:

engineering; evolutionary analysis; hypothesis testing; natural selection; software; statistical inference

PMID:
31504749
DOI:
10.1093/molbev/msz197

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