GSR: Simulator - msHOT

Basic Package Attributes
AttributeValue
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 14 years ago
Homepagehttp://home.uchicago.edu/~rhudson1/
Citations Hudson RR, Two-locus sampling distributions and their application., Genetics, 12-01-2001 [ Abstract, cited in PMC ]
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Application
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Last evaluated11-15-2018 (702 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsSingle Nucleotide Variation,
Simulation MethodStandard Coalescent,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence, Individual Relationship,
Sequencing Reads
File FormatMS,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck,
Gene FlowStepping Stone Models, Island Models,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates (Simulate recombination hotspts), Gene Conversion Allowed,
Mutation Models
Events AllowedVarying Demographic Features,
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix, Solaris,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

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]


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