Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 37, Issue 1, Pages 295-299Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msz197
Keywords
evolutionary analysis; natural selection; hypothesis testing; statistical inference; software engineering
Funding
- NIH/NIGMS [R01 GM093939, U01 GM110749]
- NIH/NIAID [R01 AI134384]
- NIH/NIEHS [T32 GM081057]
- Alan Turing Institute via an Engineering and Physical Sciences Research Council grant [EP/510129/1]
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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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