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RESEARCH PRODUCT
Importance sampling for Lambda-coalescents in the infinitely many sites model
Jochen BlathMatthias BirknerMatthias Steinrueckensubject
Class (set theory)ComputationSample (statistics)62F99 (Primary) 62P10 92D10 92D20 (Secondary)LambdaArticleSampling StudiesCoalescent theoryEvolution MolecularGene FrequencyFOS: MathematicsQuantitative Biology::Populations and EvolutionAnimalsQuantitative Biology - Populations and EvolutionEcology Evolution Behavior and Systematicscomputer.programming_languageMathematicsDiscrete mathematicsModels GeneticBETA (programming language)Probability (math.PR)Populations and Evolution (q-bio.PE)Markov ChainsGenetics PopulationPerformance comparisonFOS: Biological sciencesMutationcomputerMonte Carlo MethodMathematics - ProbabilityImportance samplingdescription
We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et. al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavar\'e (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et. al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2011-05-09 |