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GSR: Simulator - SeqSIMLA
| Attribute | Value |
|---|---|
| Title | SeqSIMLA |
| Short Description | SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. |
| Long Description | SeqSIMLA can simulate sequence data in families with multiple affected and unaffected siblings or unrelated case-control data under different disease models. SeqSIMLA accepts a population of sequences generated by other sequence generators. We implemented two disease models, in which the user can flexibly specify the number of disease loci, effect sizes or population attributable risk, disease prevalence, and risk or protective loci. We also implemented a quantitative trait model, in which the user can specify the number of quantitative trait loci (QTL), proportions of variance explained by the QTL, and genetic models. In 2014, we extended SeqSIMLA to create SeqSIMLA2, which can simulate correlated traits and considers the shared environmental effects. SeqSIMLA2 can also simulate prespecified large pedigree structures. There are no restrictions on the number of individuals that can be simulated in a pedigree. In 2015, we implemented SeqSIMLA2_exact, which can simulate sequences with multiple disease sites in large pedigrees with given disease status for each pedigree member, assuming that the disease prevalence is low. |
| Version | 1.1 |
| Project Started | 2013 |
| Last Release | 8 years, 7 months ago |
| Homepage | http://seqsimla.sourceforge.net/ |
| Citations |
|
| GSR Certification | Accessibility |
| Last evaluated | 08-09-2018 (2074 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, |
| Variations | Biallelic Marker, Single Nucleotide Variation, |
| Simulation Method | Standard Coalescent, Resample Existing Data, Gene dropping, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, |
| Sequencing Reads | |
| File Format | Linkage, |
| Sample Type | Random or Independent, Sibpairs, Trios and Nuclear Families, Extended or Complete Pedigrees, Case-control, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | C or C++, Java, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 3
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used SeqSIMLA.
2019
Zhang X, Basile AO, Pendergrass SA, Ritchie MD, Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico., BMC Bioinformatics, 01-22-2019 [Abstract]
2018
Baron RV, Stickel JR, Weeks DE, The Mega2R package: R tools for accessing and processing genetic data in common formats., F1000Res, 08-29-2018 [Abstract]