GSR: Simulator - SMARTPOP
Attribute | Value |
---|---|
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 |
Homepage | http://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 |
Last evaluated | 10-01-2020 (1268 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA, |
Variations | Single Nucleotide Variation, |
Simulation Method | Forward-time, |
Input | |
Data Type | Saved simulation, Other, |
File format | Program Specific, |
Output | |
Data Type | Genotype or Sequence, Diversity Measures, |
Sequencing Reads | Other, |
File Format | Arlequin, Fasta or Fastq, Program Specific, |
Sample Type | Random or Independent, |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
Gene Flow | |
Spatiality | |
Life Cycle | Discrete Generation Model, |
Mating System | Random Mating, Monogamous, Polygamous, Haplodiploid, Other, |
Fecundity | Randomly Distributed, |
Natural Selection | |
Determinant | |
Models | |
Recombination | |
Mutation Models | Markov DNA Evolution Models, |
Events Allowed | Varying Demographic Features, Population Events, Change of Mating Systems, Other, |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
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]