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HyPhy consists of three major components: a high-level programming language designed to facilitate the rapid implementation of new statistical methods for molecular evolutionary analysis; a collection of pre-written anal-yses for carrying out widely-used molecular evolutionary methods; a graphical user interface that allows users to quickly and ...
Aug 27, 2019 · HYpothesis testing using PHYlogenies (HyPhy) is an open-source software package for comparative sequence analysis using stochastic evolutionary models for codon, protein, nucleotide, and other discrete character data.
- Sergei L Kosakovsky Pond, Art F Y Poon, Ryan Velazquez, Steven Weaver, N Lance Hepler, Ben Murrell, ...
- 10.1093/molbev/msz197
- 2020
- Mol Biol Evol. 2020 Jan; 37(1): 295-299.
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HyPhy consists of three major components: a high-level programming guage designed to facilitate the rapid implementation of new statistical ods for molecular evolutionary analysis; a collection of prewritten for carrying out widely used molecular evolutionary methods; and a user interface that allows users to quickly and interactively analyze da...
- Overview#
- Brief History#
- Design Philosophy#
- Features#
HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. It features a rich scripting language for limitless customization of analyses. Additionally, HyPhy feat...
HyPhy grew out of the collaboration between Spencer Muse and Sergei Kosakovsky Pond that commenced in 1997 and continues to this day, with many additional collaborators, including Art Poon, Simon Frost, Steven Weaver, Stephanie Spielman, Lance Hepler, Martin Smith, Konrad Scheffler, Wayne Delport, Ben Murrell, and Joel Wertheim. HyPhy was originall...
HyPhy was designed to allow the specification and fitting of a broad class of continuous-time discrete-space Markov models of sequence evolution. To implement these models, HyPhy provides its own scripting language - HBL, or HyPhy Batch Language (see an example), which can be used to develop custom analyses or modify existing ones. Importantly, it ...
Support for arbitrary sequence data, including nucleotide, amino-acid, codon, binary, count (microsattelite) data, including multiple partitions mixing differen data types.Complex models of rate variation, including site-to-site, branch-to-branch, hidden markov model (autocorrelated rates), between/within partitions, and co-varion type models.Fast numerical fitting routines, supporting parallel and distributed execution.A broad collection of pre-defined evolutionary models.HyPhy is most commonly used for characterizing the evolutionary process, in particular: Detecting signatures of selection. Estimating evolutionary rates. Comparing different evolutionary models. Fitting custom models to sequence alignments. Characterizing selective pressures.
Apr 1, 2005 · The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies...
Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Available Versions
