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

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  • RoyChoudhury, Arindam
  • Thompson, Elizabeth A.

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.

Suggested Citation

  • RoyChoudhury, Arindam & Thompson, Elizabeth A., 2012. "Ascertainment correction for a population tree via a pruning algorithm for likelihood computation," Theoretical Population Biology, Elsevier, vol. 82(1), pages 59-65.
    • Handle: RePEc:eee:thpobi:v:82:y:2012:i:1:p:59-65
    DOI: 10.1016/j.tpb.2012.04.002
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