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Aug 27, 2019 · 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.
Using HyPhy to detect selection. These tutorials outline how to prepare data and execute analyses in HyPhy's suite of methods for detecting natural selection in protein-coding alignments. Specifically, this tutorial explains how to use the current release of HyPhy from the command line .
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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.
- 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 (/ ˈ h aɪ f aɪ / HY-fy) is a free multiplatform (Mac, Windows and UNIX) computational phylogenetics software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies".
Description. Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Available Versions. For more information, please check its website: https://biocontainers.pro/tools/hyphy and its home page on Github. Commands. hyphy. Module.
Video tutorials for DataMonkey.org and HyPhy. Using HyPhy as a Command Line Tool. Using HyPhy Interactive Command Line Prompt to Detect Selection. Using HyPhy-GUI to Detect Selection. Labeling branches with phylotree. Information, documentation, and news about the HyPhy software package.
