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.
Original language | English (US) |
---|---|
Article number | e0139047 |
Journal | PloS one |
Volume | 10 |
Issue number | 9 |
DOIs | |
State | Published - Sep 23 2015 |
Externally published | Yes |
All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
- Agricultural and Biological Sciences(all)
- General