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  1. hyphy.org › aboutHyPhy - Hypothesis Testing using Phylogenies - Information ...

    Overview. HyPhy ( 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.

  2. www.ncbi.nlm.nih.gov › pmc › articlesHyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis ...

    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.

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  4. hyphy.org › getting-startedHyPhy - Hypothesis Testing using Phylogenies - Information ...

    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.

  5. hyphy.org › tutorialsHyPhy - Hypothesis Testing using Phylogenies - Information ...

    Tutorials. 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.

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  7. en.wikipedia.org › wiki › HYPHY_(software)HYPHY (software) - Wikipedia

    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.

    • Sergei L Kosakovsky Pond, Art FY Poon, Steven Weaver, N. Lance Hepler, Martin Smith.
    • English

  8. msi.umn.edu › our-resources › msi-softwarehyphy | Minnesota Supercomputing Institute

    Sep 13, 2023 · Software Description. HyPhy stands for hypothesis testing using phylogenies. 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 ...

  9. github.com › veg › hyphyGitHub - veg/hyphy: HyPhy: Hypothesis testing using Phylogenies

    HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.

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