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International Symposium on Bioinformatics Research and Applications

ISBRA 2009: Bioinformatics Research and Applications pp 209–220Cite as

Exact Computation of Coalescent Likelihood under the Infinite Sites Model

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5542))

Abstract

Coalescent likelihood is the probability of observing the given population sequences under the coalescent model. Computation of coalescent likelihood under the infinite sites model is a classic problem in coalescent theory. Existing methods are based on either importance sampling or Markov chain Monte Carlo. In this paper, we develop a simple method that can compute the exact coalescent likelihood for many datasets of moderate size, including a real biological data whose likelihood was previously thought to be difficult to compute exactly. Simulations demonstrate that the practical range of exact coalescent likelihood computation is significantly larger than what was previously believed.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, U.S.A.

    Yufeng Wu

Authors
  1. Yufeng Wu
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Editors and Affiliations

  1. Computer Science & Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 2155, CT 06269, Storrs, USA

    Ion Măndoiu

  2. Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, 11200 SW 8th Street, Room ECS254, University Park, FL 33199, Miami, USA

    Giri Narasimhan

  3. Department of Computer Science, Georgia State University, P.O. Box 3994, GA 30302-3994, Atlanta, USA

    Yanqing Zhang

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© 2009 Springer-Verlag Berlin Heidelberg

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Wu, Y. (2009). Exact Computation of Coalescent Likelihood under the Infinite Sites Model. In: Măndoiu, I., Narasimhan, G., Zhang, Y. (eds) Bioinformatics Research and Applications. ISBRA 2009. Lecture Notes in Computer Science(), vol 5542. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01551-9_21

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  • DOI: https://doi.org/10.1007/978-3-642-01551-9_21

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-01550-2

  • Online ISBN: 978-3-642-01551-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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