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GSR: Simulator - cosi2
| Attribute | Value |
|---|---|
| Title | cosi2 |
| Short Description | an efficient coalescent simulator with support for simulating selection |
| Long Description | cosi2 is an efficient coalescent simulator with support for selection, population structure, variable recombination rates, and gene conversion. It supports exact and approximate simulation modes. |
| Version | 2.0 |
| Project Started | 2014 |
| Last Release | 9 years, 11 months ago |
| Homepage | https://software.broadinstitute.org/mpg/cosi2/ |
| Citations | Shlyakhter I, Sabeti PC, Schaffner SF, Cosi2: an efficient simulator of exact and approximate coalescent with selection., Bioinformatics, 12-01-2014 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 10-06-2016 (2746 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Standard Coalescent, Exact Coalescent, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | MS, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Exponential Growth or Decline, Bottleneck, |
| Gene Flow | Admixed Population, Other, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | Other, |
| Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
| Mutation Models | Two-allele Mutation Model, Infinite-sites Model, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, Solaris, |
| Language | C or C++, |
| License | |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used cosi2.
2016
Deschamps M, Laval G, Fagny M, Itan Y, Abel L, Casanova JL, Patin E, Quintana-Murci L, Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes., Am J Hum Genet, 01-07-2016 [Abstract]
Jacobs GS, Sluckin TJ, Kivisild T, Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps., Genetics, 08-01-2016 [Abstract]
2015
Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, et al., Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates., Am J Hum Genet, 12-03-2015 [Abstract]