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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. The HYPHY name is an abbreviation for "HYpothesis testing using PHYlogenies".
Use HyPhy from MEGA# The popular MEGA software package has begun integrating HyPhy tools into the MEGA interface. The current release has a limited set of HyPhy tools but this is expected to be expanded in the future. Use HyPhy for software/pipeline development# Compile HyPhy as a library that can be accessed via Python, R, or other language ...
Hypothesis Testing using Phylogenies An open-source software package. for comparative sequence analysis. using stochastic evolutionary models. Download
Aug 27, 2019 · 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 can be run on a desktop, either as a command-line tool for access to its complete functionality, or via a simple Electron-based graphical user ...
- 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.
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. It features a rich scripting language for limitless customization of analyses.
HyPhy provides a suite of tools for analyzing phylogenetic sequence data, in particular for inferring the strength of selection from sequence data. In addition, HyPhy features a flexible batch language for implementing and customizing discrete state Markov models in a phylogenetic framework.
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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.
