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Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580465/ https://www.ncbi.nlm.nih.gov/pubmed/26397960 http://dx.doi.org/10.1371/journal.pone.0139047 |
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author | Spielman, Stephanie J. Wilke, Claus O. |
author_facet | Spielman, Stephanie J. Wilke, Claus O. |
author_sort | Spielman, Stephanie J. |
collection | PubMed |
description | We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve. |
format | Online Article Text |
id | pubmed-4580465 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-45804652015-10-01 Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies Spielman, Stephanie J. Wilke, Claus O. PLoS One Research Article We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated into Python bioinformatics pipelines, Pyvolve can simulate sequences according to most standard models of nucleotide, amino-acid, and codon sequence evolution. All model parameters are fully customizable. Users can additionally specify custom evolutionary models, with custom rate matrices and/or states to evolve. This flexibility makes Pyvolve a convenient framework not only for simulating sequences under a wide variety of conditions, but also for developing and testing new evolutionary models. Pyvolve is an open-source project under a FreeBSD license, and it is available for download, along with a detailed user-manual and example scripts, from http://github.com/sjspielman/pyvolve. Public Library of Science 2015-09-23 /pmc/articles/PMC4580465/ /pubmed/26397960 http://dx.doi.org/10.1371/journal.pone.0139047 Text en © 2015 Spielman, Wilke http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Spielman, Stephanie J. Wilke, Claus O. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies |
title | Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies |
title_full | Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies |
title_fullStr | Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies |
title_full_unstemmed | Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies |
title_short | Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies |
title_sort | pyvolve: a flexible python module for simulating sequences along phylogenies |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580465/ https://www.ncbi.nlm.nih.gov/pubmed/26397960 http://dx.doi.org/10.1371/journal.pone.0139047 |
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