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SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

Foll, Matthieu
Published in Bioinformatics. 2010, vol. 26, no. 23, p. 2993-2994
Abstract SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios. The spatially explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources. A coalescent-based approach is used to generate genetic markers mostly used in population genetics studies (DNA sequences, SNPs, STRs or RFLPs). Various combinations of independent, fully or partially linked genetic markers can be produced under a recombination model based on the ancestral recombination graph. Competition between two populations (or species) can also be simulated with user-defined levels of admixture between the two populations. SPLATCHE2 may be used to generate the expected genetic diversity under complex demographic scenarios and can thus serve to test null hypotheses. For model parameter estimation, SPLATCHE2 can easily be integrated into an Approximate Bayesian Computation (ABC) framework. Availability and implementation: SPLATCHE2 is a C++ program compiled for Windows and Linux platforms. It is freely available at www.splatche.com, together with its related documentation and example data. CONTACT: mathias.currat@unige.ch
Keywords ModelingSimulationDemographyGeneticsCoalescentEcologyPopulationSoftwareProgram
PMID: 20956243
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Research groups TIGERS
Unité d'anthropologie
Envirospace Lab
ISE Pôle Sciences
ISE Pôle Informatique environnementale
ISE Biodiversité
(ISO format)
RAY, Nicolas et al. SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. In: Bioinformatics, 2010, vol. 26, n° 23, p. 2993-2994. doi: 10.1093/bioinformatics/btq579 https://archive-ouverte.unige.ch/unige:14234

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Deposited on : 2011-01-28

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