Computer simulations: tools for population and evolutionary genetics - PubMed (original) (raw)

Review

. 2012 Jan 10;13(2):110-22.

doi: 10.1038/nrg3130.

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• PMID: 22230817
• DOI: 10.1038/nrg3130

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Review

Computer simulations: tools for population and evolutionary genetics

Sean Hoban et al. Nat Rev Genet. 2012.

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Abstract

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data produced by simulations, along with greater availability of population-genomics data, are transforming genetic epidemiology, anthropology, evolutionary and population genetics and conservation. In this Review of the state-of-the-art of simulation software, we identify applications of simulations, evaluate simulator capabilities, provide a guide for their use and summarize future directions.

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References

1. 1. Evolution. 2004 May;58(5):913-24 - PubMed
2. 1. PLoS One. 2008;3(10):e3395 - PubMed
3. 1. Genet Epidemiol. 1998;15(3):251-62 - PubMed
4. 1. Mol Ecol Resour. 2010 Sep;10(5):886-901 - PubMed
5. 1. Curr Genomics. 2010 Mar;11(1):58-61 - PubMed

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