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GSR: Simulator - SLiM
| Attribute | Value |
|---|---|
| Title | SLiM |
| Short Description | A framework for implementing forward genetic simulations, including an interactive development environment and a highly flexible scripting language. |
| Long Description | SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex eco-evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations. For macOS, Linux, and Windows (native and WSL) users, we also provide a graphical user interface for easy simulation set-up, interactive runtime control, and dynamical visualization of simulation output. |
| Keywords | population genetic simulator, forward-time, multiple species, coevolutionary dynamics |
| Version | 5.1 |
| Project Started | 2013 |
| Last Release | 3 weeks, 1 day ago |
| Homepage | https://messerlab.org/slim/ |
| Citations |
|
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Sept. 7, 2016 (3293 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA, Protein Sequence, Phenotype, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Amino acid variation, Microsatellite, Insertion and Deletion, CNV, Inversion and Rearrangement, Alternative Splicing, Missing Genotypes, Genotype or Sequencing Error, Other, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, Empirical, Ancestral Sequence, Saved simulation, Reference genome, Other, |
| File format | MS, Tree Sequence, Program Specific, Other, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Mutation, Linkage Disequilibrium, Diversity Measures, Fitness, |
| Sequencing Reads | Other, |
| File Format | Fasta or Fastq, MS, VCF, Tree Sequence, Program Specific, Other, |
| Sample Type | Random or Independent, Sibpairs, Trios and Nuclear Families, Extended or Complete Pedigrees, Case-control, Longitudinal, Other, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Sex-linked, 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, Continent-Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, Admixed Population, User-defined Matrix, Other, |
| Spatiality | Discrete Models, Continuous Models, Landscape Factors, |
| Life Cycle | Discrete Generation Model, Age structured, Overlapping Generation, User-Defined transition matrices, |
| Mating System | Random Mating, Monogamous, Polygamous, Haplodiploid, Selfing, Age- or Stage-Specific, Assortative or Disassortative, Other, |
| Fecundity | Constant Number, Randomly Distributed, Individually Determined, Influenced by Environment, Other, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Codon-based, Fitness of Offspring, Phenotypic Trait, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Disruptive, Phenotype Threshold, Frequency-Dependent, Other, |
| Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
| Mutation Models | Two-allele Mutation Model, Markov DNA Evolution Models, k-Allele Model, Infinite-allele Model, Infinite-sites Model, Stepwise Mutation Model, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, Others, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems, Other, |
| Other | Phenogenetic, Polygenic background, |
| Interface | Command-line, Graphical User Interface, Integrated Development Environment, Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, Other, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 6
Number of Non-Primary Citations: 0
No example publication using SLiM has been provided.
Please propose new citations if you are aware of publications that use this software.