Ascertainment correction for a population tree via a pruning algorithm for likelihood computation

Arindam RoyChoudhury and Elizabeth A. Thompson

Theoretical Population Biology, 2012, vol. 82, issue 1, 59-65

Abstract: We present a method for correcting ascertainment-bias in a coalescent-based likelihood for population trees. Our method is computationally simple and fast. To correct for the bias we compute the probability of allele-counts conditioned on the locus being included. This conditional probability is simply the uncorrected likelihood divided by the inclusion probability. A modification of a pruning algorithm is introduced so that the inclusion probability can be computed with a single run of the algorithm. Our computation is exact and avoids Monte-Carlo based methods.

Keywords: Phylogeny; Population tree; Pruning; Ascertainment; Likelihood (search for similar items in EconPapers)
Date: 2012
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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:82:y:2012:i:1:p:59-65

DOI: 10.1016/j.tpb.2012.04.002

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