Jonathan Eisen likes a paper on new software for simulating genome evolution. The paper, published in Genome Biology, comes out of Ian Holmes' lab at Berkeley. His team has written three new open-source programs that address inherent problems in current 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," says the abstract, and all three perform better than the leading neutral DNA simulator (DAWG) in benchmarks. You can download the programs at BioWiki.
Simulating Genome Evolution, Made Easier
Nov 22, 2008