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The Kernel of Maximum Agreement Subtrees

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Bioinformatics Research and Applications (ISBRA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6674))

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Abstract

A Maximum Agreement SubTree (MAST) is a largest subtree common to a set of trees and serves as a summary of common substructure in the trees. A single MAST can be misleading, however, since there can be an exponential number of MASTs, and two MASTs for the same tree set do not even necessarily share any leaves. In this paper we introduce the notion of the Kernel Agreement SubTree (KAST), which is the summary of the common substructure in all MASTs, and show that it can be calculated in polynomial time (for trees with bounded degree). Suppose the input trees represent competing hypotheses for a particular phylogeny. We show the utility of the KAST as a method to discern the common structure of confidence, and as a measure of how confident we are in a given tree set.

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Author information

Authors and Affiliations

  1. Department of Mathematics and Statistics, University of Ottawa, Ontario, K1N 6N5, Canada

    Krister M. Swenson & David Sankoff

  2. Department of Biology, University of Ottawa, Ontario, K1N 6N5, Canada

    Eric Chen

  3. LaCIM, UQAM, Montréal, Québec, H3C 3P8, Canada

    Krister M. Swenson

  4. Sandia National Laboratories, Albuquerque, New Mexico, USA

    Nicholas D. Pattengale

Authors
  1. Krister M. Swenson
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  2. Eric Chen
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  3. Nicholas D. Pattengale
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  4. David Sankoff
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, 77843-3112, College Station, TX, USA

    Jianer Chen

  2. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

  3. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Alexander Zelikovsky

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© 2011 Springer-Verlag Berlin Heidelberg

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Swenson, K.M., Chen, E., Pattengale, N.D., Sankoff, D. (2011). The Kernel of Maximum Agreement Subtrees. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_15

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  • DOI: https://doi.org/10.1007/978-3-642-21260-4_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21259-8

  • Online ISBN: 978-3-642-21260-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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