GSR: Simulator - scrm

Basic Package Attributes
AttributeValue
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 7 months, 2 weeks ago
Homepagehttps://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 CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated05-09-2017 (1257 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodStandard Coalescent,
Input
Data Type
File formatMS,
Output
Data TypeGenotype or Sequence,
Sequencing ReadsOther,
File FormatMS,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck,
Gene FlowStepping Stone Models, Island Models, Admixed Population, User-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsInfinite-sites Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Varying Genetic Features,
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++, R,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

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]


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