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.
authors.affiliation: Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States of America.
authors.forename: Stephanie J
authors.initials: SJ
authors.lastname: Spielman
authors.affiliation: Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States of America.
authors.forename: Claus O
authors.initials: CO
authors.lastname: Wilke
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D003198:Computer Simulation; D023281:Genomics / Q000379:methods; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny