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Activity Number:
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111
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Type:
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Contributed
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Date/Time:
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Monday, August 7, 2006 : 8:30 AM to 10:20 AM
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Sponsor:
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Biometrics Section
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| Abstract - #306509 |
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Title:
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A Two-Stage Peeling Algorithm and Its Applications to Phylogeny
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Author(s):
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Arindam RoyChoudhury*+ and Joseph Felsenstein and Elizabeth A. Thompson
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Companies:
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University of Washington and University of Washington and University of Washington
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Address:
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Box 354322, Seattle, WA, 98195,
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Keywords:
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coalescent ; divergence time ; maximum likelihood ; peeling ; phylogeny ; SNP
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Abstract:
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We developed a peeling algorithm for likelihood estimation of phylogenetic tree for populations within same species. Our method utilizes the differences accumulated from random genetic drift in allelic count data from single nucleotide polymorphisms. The likelihood computation involves two steps. First, the likelihood is maximized across branch lengths for a given tree topology; then likelihood is maximized across topologies. Our focus is the first step. The peeling algorithm translates the data at the tip of the tree to arrays of probabilities at the root; at the root, the arrays determine the likelihood. The arrays consist of probabilities related to the number of coalescences and allelic counts among the partially coalesced lineages. Tracking these probabilities requires a two-stage algorithm. Our computation is exact, and avoids time consuming Monte Carlo methods.
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