GSR: Simulator - cosi2

Basic Package Attributes
AttributeValue
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 6 years, 5 months ago
Homepagehttps://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
Documentation
Application
Support

Last evaluated10-06-2016 (1472 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent, Exact Coalescent,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatMS,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesExponential Growth or Decline, Bottleneck,
Gene FlowAdmixed Population, Other,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
ModelsOther,
RecombinationUniform, Varying Recombination Rates, Gene Conversion Allowed,
Mutation ModelsTwo-allele Mutation Model, Infinite-sites Model,
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix, Solaris,
LanguageC or C++,
License
GSR CertificationAccessibility, Documentation, Application,

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]


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