BOTTLENECK

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Title BOTTLENECK
Short Description Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies
Long Description The program BOTTLENECK computes for each population sample and for each locus the distribution of the heterozygosity expected from the observed number of alleles (k), given the sample size (n) under the assumption of mutation-drift equilibrium. This distribution is obtained through simulating the coalescent process of n genes under two possible mutation models, the IAM and the SMM. This enables the computation of the average (Hexp) which is compared to the observed heterozygosity (Hobs, in the sense of Nei's gene diversity) to establish whether there is an heterozygosity excess or deficit at this locus. In addition, the standard deviation (SD) of the mutation-drift equilibrium distribution of the heterozygosity is used to compute the standardized difference for each locus ((Hobs-Hexp)/SD). The distribution obtained through simulation enables also the computation of a P-value for the observed heterozygosity.
Version 1.2.02
Project Started 1999
Last Release 19 years, 7 months ago
Homepagehttp://www1.montpellier.inra.fr/CBGP/software/Bottleneck/bottleneck.html
Citations Cornuet JM, Luikart G, Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data., Genetics, Dec. 1, 1996 [Abstract, cited in PMC ]
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