Importance sampling for Lambda-coalescents in the infinitely many sites model

Matthias Birkner, Jochen Blath and Steinrücken, Matthias

Theoretical Population Biology, 2011, vol. 79, issue 4, 155-173

Abstract: 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 Tavaré (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.

Keywords: Lambda-coalescent; Infinitely many sites model; Likelihood estimation; Importance sampling; Population genetics (search for similar items in EconPapers)
Date: 2011
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Citations: View citations in EconPapers (2)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:79:y:2011:i:4:p:155-173

DOI: 10.1016/j.tpb.2011.01.005

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