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Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

Avinash Varadarajan1, Robert K Bradley2 and Ian H Holmes23*

Author Affiliations

1 Computer Science Division, University of California, Berkeley, CA 94720-1776, USA

2 Biophysics Graduate Group, University of California, Berkeley, CA 94720-3200, USA

3 Department of Bioengineering, University of California, Berkeley, CA 94720-1762, USA

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Genome Biology 2008, 9:R147  doi:10.1186/gb-2008-9-10-r147

Published: 8 October 2008

Abstract

Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools webcite.