GSR: Simulator - GAMETES

Basic Package Attributes
AttributeValue
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 8 years, 9 months ago
Homepagehttps://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
Documentation
Application
Support

Last evaluated02-27-2019 (597 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Sex Chromosomes,
VariationsBiallelic Marker, Single Nucleotide Variation, Missing Genotypes (Upcoming),
Simulation MethodOther (Mathematically determined based on specification of constraints and random seeding),
Input
Data TypeAllele Frequencies, Other (The user may use a real dataset within which to generate a simulated complex genetic relationship),
File formatOther (Tab-delimited text files),
Output
Data TypeGenotype or Sequence, Phenotypic Trait (Affection status),
Sequencing ReadsOther (Model difficulty metrics for simulated models used in the simulated data.),
File Format
Sample TypeRandom or Independent, Case-control,
Phenotype
Trait TypeBinary or Qualitative (Binary),
DeterminantsMultiple 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
ModelsEpistasis,
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line, Graphical User Interface,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageJava,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

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