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GSR: Simulator - Geonomics
| Attribute | Value |
|---|---|
| Title | Geonomics |
| Short Description | A Python package for simulation of genomic evolution on complex and dynamic landscapes |
| Long Description | Geonomics is a Python package for forward-time, individual-based, continuous-space, population genomic simulations on complex and dynamic landscapes. Geonomics models are parameterized by way of an informatively annotated parameters file that provides the user a straightforward means of building models of arbitrary complexity while offering reasonable default settings and “off switches” for parameters and components unrelated to the user’s interests. Models consist of 1) a landscape with one or more environmental layers, each of which can undergo arbitrarily complex environmental change events and 2) one or more species having genomes with realistic architecture and any number of associated phenotypes. Species undergo non-Wright-Fisher evolution in continuous space, with localized mating and mortality, such that species-level phenomena and simulation dynamics are emergent properties of a model’s parameterization. Evolution is comprehensively tracked by way of tskit data structures that record the complete spatial pedigree, providing for the customizable output of rich, 3D data sets in a variety of common formats, including VCF and FASTA for genomic data, GeoTiff for landscape data, and CSV, Shapefile, and GeoJSON for individuals’ nongenomic data (location, environmental values, phenotypes, age, and sex). All of this allows Geonomics to produce realistic landscape genomic results useful for a wide variety of theoretical and empirical purposes. |
| Keywords | landscape genomics, quantitative trait, multiple traits, environmental change, spatial simulation, agent-based simulation, population dynamics, life history, spatial pedigree, spatially varying selection, non-Wright-Fisher, Python, scripting, visualization |
| Version | 1.3 |
| Project Started | 2019 |
| Last Release | 3 years, 8 months ago |
| Homepage | https://github.com/erthward/geonomics |
| Citations | Terasaki Hart DE, Bishop AP, Wang IJ, Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations., Mol Biol Evol, Sept. 27, 2021 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | March 8, 2022 (1262 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, |
| Variations | Biallelic Marker, Single Nucleotide Variation, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, Other, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Phylogenetic Tree, Demographic, Linkage Disequilibrium, Diversity Measures, Fitness, |
| Sequencing Reads | Other, |
| File Format | Fasta or Fastq, VCF, Program Specific, Other, |
| Sample Type | Random or Independent, Other, |
| Phenotype | |
| Trait Type | Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | Influenced by Environmental Factors, Other, |
| Spatiality | Continuous Models, Landscape Factors, |
| Life Cycle | Discrete Generation Model, Age structured, Overlapping Generation, |
| Mating System | Random Mating, Polygamous, Age- or Stage-Specific, Other, |
| Fecundity | Constant Number, Randomly Distributed, |
| Natural Selection | |
| Determinant | Phenotypic Trait, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Other, |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, Infinite-sites Model, Others, |
| Events Allowed | Varying Demographic Features, Population Events, Other, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | Python, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using Geonomics has been provided.
Please propose new citations if you are aware of publications that use this software.