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

Theoretical Population Biology
Arindam RoyChoudhury, Elizabeth A Thompson

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.

References

Jan 1, 1973·Human Heredity·R C Elston
Apr 12, 2003·Theoretical Population Biology·Rasmus Nielsen, James Signorovitch
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
Oct 28, 2005·Genome Research·Andrew G ClarkRasmus Nielsen
Sep 11, 2008·Genetics·Arindam RoyChoudhuryElizabeth A Thompson
Mar 17, 2012·Molecular Biology and Evolution·David BryantArindam RoyChoudhury

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Citations

Jul 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Rohan S MehtaNoah A Rosenberg
Dec 25, 2013·Evolutionary Bioinformatics Online·Arindam Roychoudhury

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