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Bioinformatics Advance Access originally published online on March 13, 2009
Bioinformatics 2009 25(11):1440-1441; doi:10.1093/bioinformatics/btp136
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

Ambra Giovannini 1,*, Gaetano Zanghirati 1, Mark A. Beaumont 2, Lounès Chikhi 3,4 and Guido Barbujani 5

1Department of Mathematics and Math4Tech Center, University of Ferrara, via Saragat, 1, I-44100 Ferrara, Italy, 2Philip Lyle Res. Building, PO Box 68, University of Reading, Whiteknights, RG6 6BX Reading, UK, 3Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, P-2780-156 Oeiras, Portugal, 4Laboratoire Evolution et Diversité Biologique, UMR CNRS/UPS 5174, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cédex 09 France and 5Department of Biology and Evolution, University of Ferrara, via Borsari, 46, I-44100 Ferrara, Italy

*To whom correspondence should be addressed.


  Abstract

Summary: Inferring population admixture from genetic data and quantifying it is a difficult but crucial task in evolutionary and conservation biology. Unfortunately state-of-the-art probabilistic approaches are computationally demanding. Effectively exploiting the computational power of modern multiprocessor systems can thus have a positive impact to Monte Carlo-based simulation of admixture modeling. A novel parallel approach is briefly described and promising results on its message passing interface (MPI)-based C++ implementation are reported.

Availability: The software package parLEA is freely available at http://dm.unife.it/parlea.

Contact: ambra.giovannini{at}unife.it

Supplementary information: Additional information, including instructions for installation/use the original sequential LEA code and the data used in this paper, are also available in the web site.

Associate Editor: Martin Bishop

Received on October 27, 2008; revised on March 5, 2009; accepted on March 6, 2009

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