GSR: Simulator - GENOME

Basic Package Attributes
AttributeValue
Title GENOME
Short Description A rapid coalescent-based whole genome simulator
Long Description GENOME is a program to simulate sequences drawn from a population under the Wright-Fisher neutral model (Ewens 1979). It is based on a standard coalescent model (Hudson 1983, 1990; Donnelly & Tavaré 1995). Starting with the sampled sequences and moving backward in time, coalescent, recombination and migration events are simulated at each generation. These events could occur multiple times and could happen in the same generation. Each coalescent event is recorded and the resulting genealogy tree is constructed. Demographic events such as population bottlenecks and expansions or population merges and splits can also be simulated. In addition to uniform recombination rates, it is possible to allow recombination rates to vary so as to mimic the pattern of hotspots along the genome. After simulating a coalescent tree, mutations are placed along each branch. The number of mutations on each branch follows a Poisson distribution with mean equal to the product of the mutation rate and the branch length. The infinite-site mutation model is assumed, so no recurrent mutation can occur. The genealogy tree can also be output in Newick format, which is identical to that used by programs such as PHYLIP (Felsenstein 2005) and seq-gen (Rambaut & Grassly 1997). The program is written in C++ and is portable to multiple operating systems. The following sections will describe how to download and compile the program and how to specify the parameters for the program.
Version 0.2
Project Started 2007
Last Release 11 years, 8 months ago
Homepagehttp://csg.sph.umich.edu/liang/genome/
Citations Liang L, Zöllner S, Abecasis GR, GENOME: a rapid coalescent-based whole genome simulator., Bioinformatics, 06-15-2007 [ Abstract, cited in PMC ]
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Last evaluated05-17-2018 (884 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodExact Coalescent,
Input
Data Type
File formatProgram Specific,
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Mutation (From the output genealogy tree), Linkage Disequilibrium (The output position is scaled by genetic distance),
Sequencing Reads
File FormatProgram Specific, Other (Genealogy tree in newick format),
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined,
Gene FlowIsland Models,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationVarying Recombination Rates,
Mutation ModelsInfinite-sites Model,
Events AllowedPopulation Merge and Split,
Other
InterfaceCommand-line, Graphical User Interface, Script-based,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix, Solaris,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

The following 2 publications are selected examples of applications that used GENOME.

2013

Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I, The variance of identity-by-descent sharing in the Wright-Fisher model., Genetics, 03-01-2013 [Abstract]

Palamara PF, Pe'er I, Inference of historical migration rates via haplotype sharing., Bioinformatics, 07-01-2013 [Abstract]


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