Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

Stephanie J Spielman and Claus O Wilke

PLOS ONE, 2015, vol. 10, issue 9, 1-7

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.

Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0139047

DOI: 10.1371/journal.pone.0139047

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