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Briefings in Bioinformatics Advance Access published online on December 24, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn048
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Simulation of DNA sequence evolution under models of recent directional selection

Yuseob Kim and Thomas Wiehe

Corresponding author. Thomas Wiehe, Universität zu Köln, Institut für Genetik, Zülpicher Straße 47, 50674 Köln, Germany. Tel: +49-221-470-1588; Fax: +49-221-470-1630; E-mail: twiehe{at}uni-koeln.de

Computer simulation is an essential tool in the analysis of DNA sequence variation for mapping events of recent adaptive evolution in the genome. Various simulation methods are employed to predict the signature of selection in sequence variation. The most informative and efficient method currently in use is coalescent simulation. However, this method is limited to simple models of directional selection. Whole-population forward-in-time simulations are the alternative to coalescent simulations for more complex models. The notorious problem of excessive computational cost in forward-in-time simulations can be overcome by various simplifying amendments. Overall, the success of simulations depends on the creative application of some population genetic theory to the simulation algorithm.

Keywords: selective sweep, polymorphism, coalescent simulation, forward-in-time simulation, adaptive evolution, Wright–Fisher model

Submitted: July 30, 2008. Received (in revised form): October 2, 2008.


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