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An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees

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Algorithms for Computational Biology (AlCoB 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10252))

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Abstract

The previously fastest algorithm for computing the rooted triplet distance between two input galled trees (i.e., phylogenetic networks whose cycles are vertex-disjoint) runs in \(O(n^{2.687})\) time, where n is the cardinality of the leaf label set. Here, we present an \(O(n \log n)\)-time solution. Our strategy is to transform the input so that the answer can be obtained by applying an existing \(O(n \log n)\)-time algorithm for the simpler case of two phylogenetic trees a constant number of times.

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Acknowledgments

J.J. was partially funded by The Hakubi Project at Kyoto University and KAKENHI grant number 26330014.

Author information

Authors and Affiliations

  1. Laboratory of Mathematical Bioinformatics, ICR, Kyoto University, Gokasho, Uji, kyoto, 611-0011, Japan

    Jesper Jansson

  2. Department of Computing, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China

    Jesper Jansson

  3. School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore

    Ramesh Rajaby & Wing-Kin Sung

  4. NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore

    Ramesh Rajaby

  5. Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore, 138672, Singapore

    Wing-Kin Sung

Authors
  1. Jesper Jansson
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  2. Ramesh Rajaby
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  3. Wing-Kin Sung
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Corresponding author

Correspondence to Wing-Kin Sung .

Editor information

Editors and Affiliations

  1. University of Aveiro, Aveiro, Portugal

    Daniel Figueiredo

  2. Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  3. University of Aveiro, Aveiro, Portugal

    Diogo Pratas

  4. University of Extremadura, Caceres, Spain

    Miguel A. Vega-Rodríguez

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Jansson, J., Rajaby, R., Sung, WK. (2017). An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In: Figueiredo, D., Martín-Vide, C., Pratas, D., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2017. Lecture Notes in Computer Science(), vol 10252. Springer, Cham. https://doi.org/10.1007/978-3-319-58163-7_8

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  • DOI: https://doi.org/10.1007/978-3-319-58163-7_8

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-58162-0

  • Online ISBN: 978-3-319-58163-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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