GSR: Simulator - SMARTPOP

Basic Package Attributes
AttributeValue
Title SMARTPOP
Short Description Simulating Mating Alliance as a Reproductive Tactic for Populations
Long Description SMARTPOP is a fast and flexible forward-in-time simulator for population genetics. Specially developed for speed, it is available in a serial and a parallel versions. Developed for anthropological inference on human populations and eco-anthropological questions, SMARTPOP simulates individuals with sequences of sex-linked DNA (mitochondria, X and Y chromosomes) and autosomes. Studies of social dynamics are enabled using SMARTPOP flexible demographic model and social rules of mating.
Version 1.0
Homepagehttp://smartpop.sourceforge.net/
Citations Guillot EG, Cox MP, SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations., BMC Bioinformatics, 06-09-2014 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated10-01-2020 (16 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA,
VariationsSingle Nucleotide Variation,
Simulation MethodForward-time,
Input
Data TypeSaved simulation, Other,
File formatProgram Specific,
Output
Data TypeGenotype or Sequence, Diversity Measures,
Sequencing ReadsOther,
File FormatArlequin, Fasta or Fastq, Program Specific,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined,
Gene Flow
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating, Monogamous, Polygamous, Haplodiploid, Other,
FecundityRandomly Distributed,
Natural Selection
Determinant
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models,
Events AllowedVarying Demographic Features, Population Events, Change of Mating Systems, Other,
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application,

The following 5 publications are selected examples of applications that used SMARTPOP.

2019

Chung NN, Jacobs GS, Sudoyo H, Malik SG, Chew LY, Lansing JS, Cox MP, Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales., R Soc Open Sci, 08-28-2019 [Abstract]

2018

Heather L. Hawk and Jonathan B. Geller, DNA entombed in archival seashells reveals low historical mitochondrial genetic diversity of endangered white abalone Haliotis sorenseni, Marine & Freshwater Research, 10-04-2018 [Abstract]

2016

Vallée F, Luciani A, Cox MP, Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia., Genetics, 12-01-2016 [Abstract]

2015

Guillot EG, Hazelton ML, Karafet TM, Lansing JS, Sudoyo H, Cox MP, Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity., Mol Biol Evol, 09-01-2015 [Abstract]

Parreira BR, Chikhi L, On some genetic consequences of social structure, mating systems, dispersal, and sampling., Proc Natl Acad Sci U S A, 06-30-2015 [Abstract]


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