SIMCOAL

SIMCOAL Screenshot
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  • Version: 1.0
  • Publisher: cmpg.unibe.ch
  • File Size: 162.06 KB
  • Date: Nov 30, 2010
  • License: Freeware
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SIMCOAL Download
Free Download SIMCOAL 1.0

Simulate molecular genetic diversity with the help of this tool. SIMCOAL is a computer program for the simulation of molecular genetic diversity in an arbitrary number of haploid populations examined for a set of fully linked loci. It is based on the retrospective coalescent approach initially described by Kingman (1982b; 1982a), and clearly exposed in a series of other papers (Ewens 1990; Hudson 1990; Donnelly and Tavar 1995).

The coalescent backward approach does not simulate the genetic history of the whole population, like in conventional forward simulations, but rather reconstructs the gene genealogy (coalescent history) of samples of genes drawn from different demes in a population.

For neutral genes, this coalescent process essentially depends on the history and on the demography of the population, and is independent from the mutational process. In our program, we simulate mutations starting from the most recent common ancestor (MRCA) of all genes in the sample, and add them independently on all branches of the genealogy assuming a uniform and constant Poisson process. Using this two-step (coalescent-mutation) approach, many replicates of haploid samples of DNA sequences, RFLP, or microsatellite data can be simulated very quickly.

The analysis of a large number of simulated samples allows one to obtain the empirical distribution of practically any statistic that can be derived from genetic data, including statistics for which no analytical derivation is available (Hudson 1993). Typical applications of our program include the study of the effect of complex demographies on the pattern of genetic diversity within and between populations, like in the case of bottlenecks, complex cases of admixture, or metapopulation systems.

While our program generates haploid samples of genes or haplotypes, diploid data can be generated under the hypothesis of Hardy-Weinberg equilibrium by taking random pairs of haplotypes to form diploid genotypes. The program runs on compatible PC computers under Windows 9X/NT, but we provide the C++ source code that should compile under other operating systems, provided the compiler follows the latest C++ ISO committee specifications.

The license of this software is Freeware, you can free download and free use this calculator software.

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