Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
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
Genome Biology 2008, 9:R147 doi:10.1186/gb-2008-9-10-r147Published: 8 October 2008
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.