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Bioinformatics Advance Access originally published online on July 14, 2005
Bioinformatics 2005 21(18):3686-3687; doi:10.1093/bioinformatics/bti584
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

simuPOP: a forward-time population genetics simulation environment

Bo Peng * and Marek Kimmel

Department of Statistics, Rice University 6100 Main Street, MS138, Houston, TX 77005, USA

*To whom correspondence should be addressed.

Summary: simuPOP is a forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios.

Availability: simuPOP is freely available at http://simupop.sourceforge.net, distributed under GPL license.

Contact: bpeng{at}rice.edu

Received on May 13, 2005; revised on July 8, 2005; accepted on July 13, 2005

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