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Bioinformatics Advance Access published online on April 15, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn179
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Forward-time Simulations of Nonrandom Mating Populations using simuPOP

Bo Peng and Christopher I. Amos

Department of Epidemiology, The University of Texas, M. D. Anderson Cancer Center, 1155 Pressler Blvd, Houston, TX, 77030

*To whom correspondence should be addressed. Dr. Bo Peng, E-mail: bpeng{at}mdanderson.org


  Abstract

Summary: Computer simulations play an important role in studies of nonrandom mating populations. Because of implementation difficulties, only very limited types of nonrandom mating schemes are provided in the currently available simulation programs. Starting with version 0.8.5, simuPOP provides a few mating schemes that can be used to simulate arbitrary nonrandom mating models. This paper describes the concepts and methods behind these mating schemes and demonstrates their uses in a few examples, including partial self-mating, positive assortative mating, nonrandom outbreeding, and simulation of overlapping generations in age-structured populations.

Availability: simuPOP is freely available at http://simupop.sourceforge.net, distributed under a GPL license. Cited examples are in the doc/cookbook directory of a simuPOP distribution.

Contact: bpeng{at}mdanderson.org

Associate Editor: Prof. Martin Bishop

Received on March 7, 2008; revised on April 4, 2008; accepted on April 14, 2008

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