Pyvolve: a flexible Python module for simulating sequences along phylogenies

Pyvolve: a flexible Python module for simulating sequences along phylogenies
Stephanie J Spielman, Claus O Wilke
doi: http://dx.doi.org/10.1101/020214
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.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s