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GSR: Simulator - BOTTLENECK
| Attribute | Value |
|---|---|
| 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 | 25 years, 2 months ago |
| Homepage | http://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, 12-01-1996 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 03-23-2018 (2213 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, |
| Variations | Biallelic Marker, Microsatellite, |
| Simulation Method | Standard Coalescent (Conditioning by the observed number of alleles), |
| Input | |
| Data Type | |
| File format | Genepop, Other (Genetix), |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Bottleneck, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | Constant Number, |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Infinite-allele Model, Stepwise Mutation Model, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, |
| Language | Other (Delphi), |
| License | |
| GSR Certification | Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used BOTTLENECK.
2018
Souza-Shibatta L, Kotelok-Diniz T, Ferreira DG, Shibatta OA, Sofia SH, de Assumpção L, Pini SFR, Makrakis S, Makrakis MC, Genetic Diversity of the Endangered Neotropical Cichlid Fish (<i>Gymnogeophagus setequedas</i>) in Brazil., Front Genet, 01-01-2018 [Abstract]
Meng JW, He DC, Zhu W, Yang LN, Wu EJ, Xie JH, Shang LP, Zhan J, Human-Mediated Gene Flow Contributes to Metapopulation Genetic Structure of the Pathogenic Fungus <i>Alternaria alternata</i> from Potato., Front Plant Sci, 01-01-2018 [Abstract]