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

    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.

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

    Aug 27, 2019 · Introduction. 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. HyPhy is written in C++14 and implements a domain-specific scripting language (HBL, or HyPhy Batch Language ...

    • 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 › tutorialsHyPhy - Hypothesis Testing using Phylogenies - Information ...

    Information, documentation, and news about the HyPhy software package. HyPhy Hypothesis Testing using Phylogenies. HyPhy. Home News and Releases About Download

  5. www.hyphy.orgHyPhy - Hypothesis Testing using Phylogenies - Information ...

    Hypothesis Testing using Phylogenies An open-source software package. for comparative sequence analysis. using stochastic evolutionary models. Download

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

    HYPHY ( / ˈhaɪfaɪ / 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. [1] The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies". [2]

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

  8. academic.oup.com › bioinformatics › articleHyPhy: hypothesis testing using phylogenies - Oxford Academic

    Oct 27, 2004 · HyPhy was developed as a unified platform for designing, running and interpreting likelihood-based analyses of sequence alignments, with emphasis on modeling the evolutionary process and ease of use. The HyPhy package serves a number of purposes and a number of audiences. It includes (1) a simple menu-based interface to many standard methods of ...

  9. academic.oup.com › mbe › articleHyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis ...

    Aug 27, 2019 · Here, we announce the release of HyPhy version 2.5 and document how the software has been packaged for easy use in a variety of settings, optimized for larger data sets, redesigned to follow modern best practices in software design and engineering, and extended to include a broader set of evolutionary models and prepackaged analyses.

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