Abstract
Abstract Summary: We present an extension of the program SIMCOAL, which allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias. Availability: http://cmpg.unibe.ch/software/simcoal2/ Supplementary information: http://cmpg.unibe.ch/software/simcoal2/
Keywords
Coalescent theoryNucleotide diversitySoftwareComputer scienceExtension (predicate logic)Diversity (politics)Set (abstract data type)PopulationBiologyComputational biologyGeneticsHaplotypeProgramming languageAlleleGene
MeSH Terms
AlgorithmsBiological EvolutionChromosome MappingComputer SimulationGenetic VariationGeneticsPopulationModelsGeneticModelsStatisticalPolymorphismSingle NucleotideRecombinationGenetic
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Publication Info
- Year
- 2004
- Type
- article
- Volume
- 20
- Issue
- 15
- Pages
- 2485-2487
- Citations
- 262
- Access
- Closed
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Cite This
Guillaume Laval,
Laurent Excoffier
(2004).
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history.
Bioinformatics
, 20
(15)
, 2485-2487.
https://doi.org/10.1093/bioinformatics/bth264
Identifiers
- DOI
- 10.1093/bioinformatics/bth264
- PMID
- 15117750