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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 ...
- Overview#
- Brief History#
- Design Philosophy#
- Features#
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. Additionally, HyPhy feat...
HyPhy grew out of the collaboration between Spencer Muse and Sergei Kosakovsky Pond that commenced in 1997 and continues to this day, with many additional collaborators, including Art Poon, Simon Frost, Steven Weaver, Stephanie Spielman, Lance Hepler, Martin Smith, Konrad Scheffler, Wayne Delport, Ben Murrell, and Joel Wertheim. HyPhy was originall...
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. Importantly, it ...
Support for arbitrary sequence data, including nucleotide, amino-acid, codon, binary, count (microsattelite) data, including multiple partitions mixing differen data types.Complex models of rate variation, including site-to-site, branch-to-branch, hidden markov model (autocorrelated rates), between/within partitions, and co-varion type models.Fast numerical fitting routines, supporting parallel and distributed execution.A broad collection of pre-defined evolutionary models.People also ask
What is hyphy used for?
What is hyphy (hypothesis testing using PHY logenies)?
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Can hyphy be run as a command line tool?
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.
- Sergei L Kosakovsky Pond, Art F Y Poon, Ryan Velazquez, Steven Weaver, N Lance Hepler, Ben Murrell, ...
- 2020
Software for molecu-lar evolution is focused disproportionately on problems relating to phyloge-netic reconstruction, with a number of outstanding comprehensive packages to choose from. On the other hand, software for addressing questions of the molecular evolutionary process tends to be found in stand-alone programs that
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.
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 ...
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]
