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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 | 5 years, 6 months 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, May 15, 2015 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | May 9, 2017 (3026 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, Jan. 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, Jan. 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, July 21, 2015 [Abstract]