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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.
- 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.
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.
- Major Features
- History
- Software/Code Availability and License
- External Links
HYPHY supports analysis of nucleotide, protein and codon sequences, using predefined standard models or user-defined models of evolution. The package supports interaction through a graphical user interface as well as a batch language to set up large and complicated analyses and process the results. HyPhy includes a versatile suite of methods to det...
The development of HyPhy started in 1997, with the first public release in 2000 and the most recent version as of December 2020 being 2.5.
HYPHY is distributed as freeware with source code released under the MIT License. Compiled binaries for Mac OS X and Windows are available for download. The source code is available so that users can compile the HyPhy application on POSIX systems. A subset of HYPHY methods for detecting adaptive evolution are also made available by the HYPHY team a...
: The HYPHY home page: The DataMonkey server, which supports a variety of HYPHY tools (at no cost).: HYPHY/DataMonkey supportHyPhy ( Hy pothesis Testing using Phy logenies) 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.
An open-source software package. for comparative sequence analysis. using stochastic evolutionary models. Download. Information, documentation, and news about the HyPhy software package.
Software: Hyphy - Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
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Sep 13, 2023 · It is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It also features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.
