Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
Open Access
- 23 September 2015
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 10 (9) , e0139047
- https://doi.org/10.1371/journal.pone.0139047
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.Keywords
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