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GSR: Simulator - msHOT
| Attribute | Value |
|---|---|
| Title | msHOT |
| Short Description | The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. |
| Long Description | This addition to Hudson’s (2002) ms, called msHOT, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region. Crossover hotspots may overlap with gene conversion hotspots, but crossover hotspots may not overlap with each other and gene conversion hotspots may not overlap with each other. |
| Project Started | 2007 |
| Last Release | 17 years, 6 months ago |
| Homepage | http://home.uchicago.edu/~rhudson1/ |
| Citations | Hudson RR, Two-locus sampling distributions and their application., Genetics, 12-01-2001 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 11-15-2018 (1976 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 | Haploid DNA Sequence, |
| Variations | Single Nucleotide Variation, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | MS, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck, |
| Gene Flow | Stepping Stone Models, Island Models, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, Varying Recombination Rates (Simulate recombination hotspts), Gene Conversion Allowed, |
| Mutation Models | |
| Events Allowed | Varying Demographic Features, |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, Solaris, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
The following 5 publications are selected examples of applications that used msHOT.
2018
Dapper AL, Payseur BA, Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium., Mol Biol Evol, 02-01-2018 [Abstract]
2016
Wall JD, Stevison LS, Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium., G3 (Bethesda), 08-09-2016 [Abstract]
2015
Smukowski Heil CS, Ellison C, Dubin M, Noor MA, Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila., Genome Biol Evol, 10-01-2015 [Abstract]
Hecker J, Prokopenko D, Lange C, Fier HL, On the Recombination Rate Estimation in the Presence of Population Substructure., PLoS One, 12-30-2015 [Abstract]
2014
Forni D, Cagliani R, Tresoldi C, Pozzoli U, De Gioia L, Filippi G, Riva S, Menozzi G, Colleoni M, Biasin M, et al., An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection., PLoS Genet, 03-27-2014 [Abstract]