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in HyPhy between a tree and a topology is an important one, as we will illustrate through later examples. 5. Likelihood Function. A combination of a data filter and a tree (which includes both topology and model information) is sufficient to define the probability of the observed data given model parameter values, i.e., the likelihood function.
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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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.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
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]
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 ...
The function is an indicator function that equals the number of nucleotide differences between codons and ; for example, and . Like most other codon models, the MG94xREV model considers only single-nucleotide codon substitutions to be instantaneous. refers to the amino-acid encoded by codon .
