Pyvolve: A flexible python module for simulating sequences along phylogenies

Stephanie J. Spielman; Claus O. Wilke

doi:10.1371/journal.pone.0139047

Pyvolve: A flexible python module for simulating sequences along phylogenies

Stephanie J. Spielman, Claus O. Wilke

Research output: Contribution to journal › Article › peer-review

49 Scopus citations

Abstract

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.

Original language	English (US)
Article number	e0139047
Journal	PloS one
Volume	10
Issue number	9
DOIs	https://doi.org/10.1371/journal.pone.0139047
State	Published - Sep 23 2015
Externally published	Yes

All Science Journal Classification (ASJC) codes

Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
General

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10.1371/journal.pone.0139047

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title = "Pyvolve: A flexible python module for simulating sequences along phylogenies",

abstract = "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.",

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Pyvolve: A flexible python module for simulating sequences along phylogenies

Abstract

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