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GSR: Simulator - scrm
| Attribute | Value |
|---|---|
| Title | scrm |
| Short Description | A coalescent simulator optimized for long sequences and large samples. |
| Long Description | The Sequential Coalescent with Recombination Model (SCRM) is a new method that efficiently and accurately approximates the coalescent with recombination. It closes the gap between current approximations and the exact model and can be used to simulate genomic-scale data sets with an essentially correct linkage structure. The efficient C++ implementation scrm is available for all major platforms and as an R package on CRAN. |
| Version | 1.7.4 |
| Project Started | 2014 |
| Last Release | 4 years, 1 month ago |
| Homepage | https://scrm.github.io/ |
| Citations | Staab PR, Zhu S, Metzler D, Lunter G, scrm: efficiently simulating long sequences using the approximated coalescent with recombination., Bioinformatics, 05-15-2015 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 05-09-2017 (2531 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | MS, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | Other, |
| File Format | MS, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck, |
| Gene Flow | Stepping Stone Models, Island Models, Admixed Population, User-defined Matrix, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Infinite-sites Model, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Varying Genetic Features, |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, R, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used scrm.
2016
Cagan A, Blass T, Identification of genomic variants putatively targeted by selection during dog domestication., BMC Evol Biol, 01-12-2016 [Abstract]
Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D, Tyler-Smith C, et al., Iron Age and Anglo-Saxon genomes from East England reveal British migration history., Nat Commun, 01-19-2016 [Abstract]
2015
Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, et al., Genomic evidence for the Pleistocene and recent population history of Native Americans., Science, 07-21-2015 [Abstract]