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GSR: Simulator - SPIP
| Attribute | Value |
|---|---|
| Title | SPIP |
| Short Description | SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user |
| Long Description | SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user. Numerous variables controlling the age structure of the population, the number of offspring produced, the variance in male and female reproductive success, survival rates of different age classes, mate fidelity, duration of simulation, etc. can be specified by the user. The program stores the pedigree of all individuals in the simulated population. This pedigree is used to simulate genetic data on sampled individuals by tracing lineages back through paternal or maternal genes within each sampled individual. Data may be simulated for an arbitrary number of loci that are assumed to be independently segregating and to not be subject to natural selection, nor linked to any selected genes. Genotypes are reported in terms of both "founder alleles" (i.e., each distinct allele amongst the founders of the pedigree is given a distinct label) and also in terms of alleles whose frequencies amongst the founding members of the pedigree may be specified by the user. |
| Version | 1.0 |
| Project Started | 2005 |
| Last Release | 19 years, 3 months ago |
| Homepage | https://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3434 |
| Citations | E. C. ANDERSON and K. K. DUNHAM, SPIP 1.0: a program for simulating pedigrees and genetic data in age‐structured populations, Molecular Ecology Note, 05-12-2005 |
| GSR Certification | Accessibility |
| Last evaluated | 09-28-2022 (563 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, |
| Variations | Biallelic Marker, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, |
| File format | Genepop, |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, Demographic, |
| Sequencing Reads | |
| File Format | Genepop, Other (Morgan), |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | User Defined, |
| Gene Flow | Sex or Age-Specific Migration Rates, User-defined Matrix, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, Monogamous, |
| Fecundity | Constant Number, |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | Varying Demographic Features, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SPIP has been provided.
Please propose new citations if you are aware of publications that use this software.