Open Genomics: Genome Evolution Simulator

Quick post here.   Cool new paper (and the software could be cool too but have not tried it yet) on simulating genome evolution.  The paper is from Ian Holmes and others at Berkeley (see his lab page on BioWiki here) and the paper can be found here in Genome Biology. Here is the 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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

2 thoughts on “Open Genomics: Genome Evolution Simulator”

  1. Hey, I was searching for a genome evolution simulator for my research proposal just now. Imagine my surprise when the first link I clicked on took me to your blog! Oh wait, I guess I should never be surprised to end up at your blog.

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