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GSR: Simulator - quantiNEMO
| Attribute | Value |
|---|---|
| Title | quantiNEMO |
| Short Description | An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population |
| Long Description | quantiNEMO is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination, and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNEMO is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc. quantiNEMO is a console program, and is coded in standard C++ using an object oriented approach, runs on any computer platform, and is distributed under an open source license. |
| Version | 1.0.4 |
| Project Started | 2008 |
| Last Release | 12 years, 7 months ago |
| Homepage | http://www2.unil.ch/popgen/softwares/quantinemo/ |
| Citations | Neuenschwander S, Hospital F, Guillaume F, Goudet J, quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation., Bioinformatics, 07-01-2008 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 06-01-2015 (3239 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, Empirical, |
| File format | Fstat, Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Diversity Measures, Fitness, |
| Sequencing Reads | Other (F-statistics), |
| File Format | Fstat, |
| Sample Type | Extended or Complete Pedigrees, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | Stepping Stone Models, Island Models, Sex or Age-Specific Migration Rates, User-defined Matrix, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, Monogamous, Polygamous, Selfing, |
| Fecundity | Constant Number, Randomly Distributed, Individually Determined, Influenced by Environment, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Phenotypic Trait, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, k-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, |
| 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, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using quantiNEMO has been provided.
Please propose new citations if you are aware of publications that use this software.