GSR: Simulator - SNPsim

Basic Package Attributes
AttributeValue
Title SNPsim
Short Description Coalescent simulation of hotspot recombination
Long Description SNPsim is a population genetic simulator that generates samples of SNP (Single Nucleotide Polymorphisms) haplotypes and diploid biallelic genotypes. It is based on the coalescent with recombination (Hudson 1983) modified by Wiuf and Posada (2003) to include recombination hotspots. SNPsim also allows for the specification of demographic periods and different mutation models.
Version 0.8
Project Started 2003
Last Release 16 years, 5 months ago
Homepagehttp://code.google.com/p/phylosoftware/
Citations Posada D, Wiuf C, Simulating haplotype blocks in the human genome., Bioinformatics, 01-22-2003 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated10-15-2020 (2 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent,
Input
Data Type
File formatProgram Specific,
Output
Data TypeGenotype or Sequence, Individual Relationship,
Sequencing Reads
File FormatProgram Specific,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, User Defined,
Gene Flow
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationVarying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model, Infinite-sites Model,
Events Allowed
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using SNPsim has been provided.

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