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Bioinformatics Advance Access published online on January 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm024
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A simulation test bed for hypotheses of genome evolution

Robert G. Beiko 1,2,* and Robert L. Charlebois 3

1Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada, and 2Institute for Molecular Bioscience and ARC Centre for Bioinformatics, Brisbane, Australia
3GenomeAtlantic, Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. Present address: sanofi pasteur, 1755 Steeles Ave. W., Toronto ON, M2R 3T4

*To whom correspondence should be addressed. Robert Beiko, E-mail: beiko{at}cs.dal.ca


  Abstract

Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution, and lateral genetic transfer. Simulation tools are essential for both the generation of data under different evolu-tionary models and the validation of analytical methods on such data. However, meaningful investigation of phenomena such as lateral genetic transfer requires the simultaneous consideration of many underlying evolutionary processes.

Results: We have developed EvolSimulator, a software package that combines nonstationary sequence and gene family evolution together with models of lateral genetic transfer, within a customiza-ble birth-death model of speciation and extinction. Here we examine simulated datasets generated with EvolSimulator using existing statistical techniques from the evolutionary literature, showing in detail each component of the simulation strategy.

Availability: Source code, manual and other information are freely available at www.bioinformatics.org.au/evolsim.

Associate Editor: Keith Crandall

Received on August 10, 2006; revised on November 23, 2006; accepted on January 22, 2007

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