SIMCOAL Simulate molecular genetic diversity with the help of this tool.
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Analyze simulation simulate genetic change Genetic System genetic information sequence diversity molecular biology tool diversity analysis diversity analyzer diversity simulate molecular dynamics analyze genotypic diversity genotypic diversity analysis Gene Diversity simulate genetic map access genomic diversity simulate genetic diversity genetic diversity simulation molecular genetic diversity haploid population simulate mutation molecular genetic genetic differentiation

SIMCOAL Description

SIMCOAL is a handy, easy to use application specially designed to help you simulate 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 Tavaré 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. This program 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 the 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 this application 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

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