GSR: Simulator - CoaSim

Basic Package Attributes
AttributeValue
Title CoaSim
Short Description CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models.
Long Description CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. It effectively constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP, micro-satellite, and other haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies. CoaSim is written in C++, Guile Scheme and Python, and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
Version 4.2.2
Project Started 2005
Last Release 9 years, 3 months ago
Homepagehttps://github.com/mailund/CoaSim
Citations Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L, CoaSim: a flexible environment for simulating genetic data under coalescent models., BMC Bioinformatics, 10-14-2005 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated02-27-2019 (598 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsSingle Nucleotide Variation, Microsatellite,
Simulation MethodStandard Coalescent,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatOther (User defined, user can write their own script),
Sample TypeRandom or Independent, Case-control (Based on genotypes at markers),
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline,
Gene FlowUser-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates, Gene Conversion Allowed,
Mutation Modelsk-Allele Model, Stepwise Mutation Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Varying Genetic Features, Other,
Other
InterfaceCommand-line, Graphical User Interface, Script-based (Through guile or python bindings),
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++, Python, Other (Guile scheme),
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application,

The following 13 publications are selected examples of applications that used CoaSim.

2014

Munch K, Mailund T, Dutheil JY, Schierup MH, A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion., Genome Res, 03-01-2014 [Abstract]

Yang T, Deng HW, Niu T, Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences., BMC Bioinformatics, 01-03-2014 [Abstract]

2012

Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH, et al., A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species., PLoS Genet, 01-01-2012 [Abstract]

2011

Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T, Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection., Genome Res, 03-01-2011 [Abstract]

2009

Besenbacher S, Mailund T, Schierup MH, Local phylogeny mapping of quantitative traits: higher accuracy and better ranking than single-marker association in genomewide scans., Genetics, 02-01-2009 [Abstract]

Pan F, McMillan L, Pardo-Manuel De Villena F, Threadgill D, Wang W, TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees., Pac Symp Biocomput, 01-01-2009 [Abstract]

Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH, Ancestral population genomics: the coalescent hidden Markov model approach., Genetics, 09-01-2009 [Abstract]

2007

Liu W, Yang T, Zhao W, Chase GA, Accounting for genotyping errors in tagging SNP selection., Ann Hum Genet, 07-01-2007 [Abstract]

Bangham J, Obbard DJ, Kim KW, Haddrill PR, Jiggins FM, The age and evolution of an antiviral resistance mutation in Drosophila melanogaster., Proc Biol Sci, 08-22-2007 [Abstract]

2006

Liu W, Zhao W, Chase GA, The impact of missing and erroneous genotypes on tagging SNP selection and power of subsequent association tests., Hum Hered, 01-01-2006 [Abstract]

Mailund T, Schierup MH, Pedersen CN, Madsen JN, Hein J, Schauser L, GeneRecon--a coalescent based tool for fine-scale association mapping., Bioinformatics, 09-15-2006 [Abstract]

Bataillon T, Mailund T, Thorlacius S, Steingrimsson E, Rafnar T, Halldorsson MM, Calian V, Schierup MH, The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers., Eur J Hum Genet, 09-01-2006 [Abstract]

Mailund T, Besenbacher S, Schierup MH, Whole genome association mapping by incompatibilities and local perfect phylogenies., BMC Bioinformatics, 10-16-2006 [Abstract]


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