Parallel LEA

A parallel software for Likelihood-based Estimation of Admixture in population genetics

Ambra Giovannini, Gaetano Zanghirati
Mark Beaumont, Lounès Chikhi, Guido Barbujani

Description

Estimating genetic population admixture is a difficult task that is shown to have meaningful applications in evolutionary and conservation Biology.
Unfortunately state-of-the-art probabilistic approaches are computationally demanding.
The ability of effectively exploiting the computational power of modern multiprocessor systems can thus contribute a beneficial impact to Monte-Carlo-based simulation of admixture modeling.

Parallel LEA is novel parallel approach for Likelihood-based Estimation of Admixture in population genetics, MPI and C++ based.

Download software and installation guide

Parallel LEA
Source code and test files: parLEA.tar.gz [Last update: Apr 21, 2009 - Bug fix in multiple-choice menu]
Installation and test guide: UserGuide.pdf
Scaling graph obtained using toy-datasets.

LEA (Likelihood-based Estimation of Admixture) - Scalar software
Source code and installation guide: lea-1.0-src.tar.gz

Contacts

• Ambra Giovannini - - Department of Mathematics, University of Ferrara, via Machiavelli, 35, I-44100 Ferrara, Italy.
• Gaetano Zanghirati - - Department of Mathematics, University of Ferrara, via Machiavelli, 35, I-44100 Ferrara, Italy.
• Mark A. Beaumont - Philip Lyle Research Building, PO Box 68, University of Reading, Whiteknights, RG6 6BX Reading, U.K.
• Lounès Chikhi - Instituto Gulbenkian de Ciencia, Rua da Quinta Grande, no6, P-2780-156 Oeiras, Portugal.
  Laboratoire Evolution et Diversité Biologique, UMR CNRS/UPS 5174, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cédex 09 France.
• Guido Barbujani - Department of Biology, University of Ferrara, via Borsari, 46, I-44100 Ferrara, Italy.

How to cite

A novel parallel approach to the likelihood-based estimation of admixture in populatin genetics
Ambra Giovannini; Gaetano Zanghirati; Mark A. Beaumont; Lounes Chikhi; Guido Barbujani
Bioinformatics 2009 25: 1440-1441

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

Useful links

LEA method:

• Estimation of Admixture Proportions: A Likelihood-Based Approach Using Markov Chain Monte Carlo.
  Lounès Chikhi, Michael W. Bruford, Mark A. Beaumont
  (read the article)
• LEA (likelihood-based estimation of admixture): a program to estimate simultaneously admixture and time since the admixture event.
  O. Langella, L. Chikhi, M. A. Beaumont
  (read the article)

Example of application:

• Y genetic data support the Neolithic demic diffusion model.
  Lounès Chikhi, Richard A. Nichols, Guido Barbujani, Mark A. Beaumont
  (read the article)
• Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci.
  Elise M.S Belle, Pierre-Alexandre Landry, Guido Barbujani
  (read the article)

Other existing methods:

• Estimating admixture proportions with microsatellites: comparison of methods based on simulated data.
  M. Choisy, P. Franck, JM. Cornuet.
  (read the article)