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GSR: Simulator - GAMETES
| Attribute | Value |
|---|---|
| Title | GAMETES |
| Short Description | Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. |
| Long Description | Rapid, user friendly software package, able to generate whole populations of “worst-case-scenario” complex genetic models with random architectures, but a user specified set of constraints (i.e. number of loci, heritability, allele frequencies, prevalence). Intended for testing and evaluating algorithms or software for their ability to detect and model epistatic interactions in the absence of any main effects. The next version will add the ability to generate heterogeneous datasets (specifically datasets which concurrently contain both epistatic and heterogeneous effects. |
| Version | 0.1.0 beta |
| Project Started | 2012 |
| Last Release | 12 years, 3 months ago |
| Homepage | https://sourceforge.net/projects/gametes/?source=navbar |
| Citations | Urbanowicz RJ, Kiralis J, Sinnott-Armstrong NA, Heberling T, Fisher JM, Moore JH, GAMETES: a fast, direct algorithm for generating pure, strict, epistatic models with random architectures., BioData Min, 10-01-2012 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 02-27-2019 (1872 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Sex Chromosomes, |
| Variations | Biallelic Marker, Single Nucleotide Variation, Missing Genotypes (Upcoming), |
| Simulation Method | Other (Mathematically determined based on specification of constraints and random seeding), |
| Input | |
| Data Type | Allele Frequencies, Other (The user may use a real dataset within which to generate a simulated complex genetic relationship), |
| File format | Other (Tab-delimited text files), |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait (Affection status), |
| Sequencing Reads | Other (Model difficulty metrics for simulated models used in the simulated data.), |
| File Format | |
| Sample Type | Random or Independent, Case-control, |
| Phenotype | |
| Trait Type | Binary or Qualitative (Binary), |
| Determinants | Multiple Genetic Markers, Gene-Gene Interaction, Environmental Factors (Only if environmental factor can be encoded as discrete with three states (as snps are encoded)), Gene-Environment Interaction (Only if environmental factor can be encoded as discrete with three states (as snps are encoded)), |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | Epistasis, |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, Graphical User Interface, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | Java, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used GAMETES.
2023
Sha Z, Chen Y, Hu T, NSPA: characterizing the disease association of multiple genetic interactions at single-subject resolution., Bioinform Adv, 02-07-2023 [Abstract]
2022
Sun Y, Gu Y, Ren Q, Li Y, Shang J, Liu JX, Guan B, MDSN: A Module Detection Method for Identifying High-Order Epistatic Interactions., Genes (Basel), 12-18-2022 [Abstract]