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Path-Difference Median Trees

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Bioinformatics Research and Applications (ISBRA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9683))

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Abstract

Synthesizing large-scale phylogenetic trees is a fundamental problem in evolutionary biology. Median tree problems have evolved as a powerful tool to reconstruct such trees. Given a tree collection, these problems seek a median tree under some problem-specific tree distance. Here, we introduce the median tree problem for the classical path-difference distance. We prove that this problem is NP-hard, and describe a fast local search heuristic that is based on solving a local search problem exactly. For an effective heuristic we devise a time efficient algorithm for this problem that improves on the best-know (naïve) solution by a factor of n, where n is the size of the input trees. Finally, we demonstrate the performance of our heuristic in a comparative study with other commonly used methods that synthesize species trees using published empirical data sets.

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Acknowledgments

The authors would like to thank the two anonymous reviewers for their constructive comments that helped to improve the quality of this work.

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Authors and Affiliations

  1. Department of Computer Science, Iowa State University, Ames, IA, 50011, USA

    Alexey Markin & Oliver Eulenstein

Authors
  1. Alexey Markin
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  2. Oliver Eulenstein
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Corresponding author

Correspondence to Oliver Eulenstein .

Editor information

Editors and Affiliations

  1. Dept. of Computer Science, Georgia State University, Atlanta, Georgia, USA

    Anu Bourgeois

  2. Centre for Disease Control & Prevention, Atlanta, Georgia, USA

    Pavel Skums

  3. Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Xiang Wan

  4. Georgia State University, Atlanta, Georgia, USA

    Alex Zelikovsky

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Markin, A., Eulenstein, O. (2016). Path-Difference Median Trees. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_18

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  • DOI: https://doi.org/10.1007/978-3-319-38782-6_18

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38781-9

  • Online ISBN: 978-3-319-38782-6

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