TY - JOUR
T1 - HyPhy 2.5 - A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
AU - Kosakovsky Pond, Sergei L.
AU - Poon, Art F.Y.
AU - Velazquez, Ryan
AU - Weaver, Steven
AU - Hepler, N. Lance
AU - Murrell, Ben
AU - Shank, Stephen D.
AU - Magalis, Brittany Rife
AU - Bouvier, Dave
AU - Nekrutenko, Anton
AU - Wisotsky, Sadie
AU - Spielman, Stephanie J.
AU - Frost, Simon D.W.
AU - Muse, Spencer V.
N1 - Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: [email protected].
PY - 2020/1/1
Y1 - 2020/1/1
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/85078566726
UR - https://www.scopus.com/pages/publications/85078566726#tab=citedBy
U2 - 10.1093/molbev/msz197
DO - 10.1093/molbev/msz197
M3 - Article
C2 - 31504749
AN - SCOPUS:85078566726
SN - 0737-4038
VL - 37
SP - 295
EP - 299
JO - Molecular biology and evolution
JF - Molecular biology and evolution
IS - 1
ER -