PT - JOURNAL ARTICLE AU - Stephanie J. Spielman AU - Claus O. Wilke TI - Pyvolve: a flexible Python module for simulating sequences along phylogenies AID - 10.1101/020214 DP - 2015 Jan 01 TA - bioRxiv PG - 020214 4099 - http://biorxiv.org/content/early/2015/06/01/020214.short 4100 - http://biorxiv.org/content/early/2015/06/01/020214.full 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.