RT Journal Article
SR Electronic
T1 Pyvolve: a flexible Python module for simulating sequences along phylogenies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 020214
DO 10.1101/020214
A1 Stephanie J. Spielman
A1 Claus O. Wilke
YR 2015
UL http://biorxiv.org/content/early/2015/06/01/020214.abstract
AB We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylogeny according to continuous-time Markov models of sequence evolution. Pyvolve incorporates most standard models of nucleotide, amino-acid, and codon sequence evolution, and it allows users to fully customize all model parameters. Pyvolve additionally allows users to specify custom evolutionary models and incorporates several novel features, including a novel rate matrix scaling algorithm and branch-length perturbations. Easily incorporated into Python bioinformatics pipelines, Pyvolve represents a convenient and flexible alternative to third-party simulation softwares. Pyvolve is an open-source project available, along with a detailed user-manual, under a FreeBSD license from https://github.com/sjspielman/pyvolve. API documentation is available from http://sjspielman.org/pyvolve.