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1. • • 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.
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     HyPhy - Hypothesis Testing using Phylogenies - Information ...

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   What is hyphy software?

   • 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.

   GitHub - veg/hyphy: HyPhy: Hypothesis testing using Phylogenies

   github.com/veg/hyphy

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   What does hyphy stand for?

   • 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. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies".

   HYPHY (software) - Wikipedia

   en.wikipedia.org/wiki/HYPHY_(software)

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   What is hyphy used for?

   • The common use of HyPhy is to fit evolutionary models and perform hypothesis testing on multiple sequence alignments with given phylogenies that are assumed to have been generated with other tools.

   HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing

   www.ncbi.nlm.nih.gov/pmc/articles/PMC8204705/

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   What is hyphy (hypothesis testing using PHY logenies)?

   • 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. It features a rich scripting language for limitless customization of analyses.

   HyPhy - Hypothesis Testing using Phylogenies - Information

   hyphy.org/about/

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

   hyphy.org › about

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   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.

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

   www.ncbi.nlm.nih.gov › pmc › articles

   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.

   • Author: Sergei L Kosakovsky Pond, Art F Y Poon, Ryan Velazquez, Steven Weaver, N Lance Hepler, Ben Murrell, ...
   • DOI: 10.1093/molbev/msz197

   • Publish Year: 2020
   • Publication: Mol Biol Evol. 2020 Jan; 37(1): 295-299.

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

   www.hyphy.org

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   An open-source software package. for comparative sequence analysis. using stochastic evolutionary models. Download. Information, documentation, and news about the HyPhy software package.

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

   github.com › veg › hyphy

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   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.

7. hyphy.org › resources › Getting_Started_With_HyPhyHyPhy: Hypothesis Testing Using Phylogenies

   hyphy.org › resources › Getting_Started_With_HyPhy

   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 ...

   • File Size: 1MB

   • Page Count: 57

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

   en.wikipedia.org › wiki › HYPHY_(software)

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   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.

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

   academic.oup.com › bioinformatics › article

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   Oct 27, 2004 · Unlike most other software packages for sequence analysis, HyPhy was designed to allow users to develop new methods of analysis quickly and easily, as opposed to simply offering a friendly interface to collections of existing methods. Also unlike most other packages, it was designed with multi-gene data sets in mind.