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An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees

  • Jesper Jansson
  • Ramesh Rajaby
  • Wing-Kin Sung
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10252)

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.

Keywords

Phylogenetic network comparison Galled tree Rooted triplet Algorithm Computational complexity 

Notes

Acknowledgments

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

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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Jesper Jansson
    • 1
    • 2
  • Ramesh Rajaby
    • 3
    • 4
  • Wing-Kin Sung
    • 3
    • 5
  1. 1.Laboratory of Mathematical Bioinformatics, ICRKyoto UniversityUji, kyotoJapan
  2. 2.Department of ComputingThe Hong Kong Polytechnic UniversityHong KongChina
  3. 3.School of ComputingNational University of SingaporeSingaporeSingapore
  4. 4.NUS Graduate School for Integrative Sciences and EngineeringNational University of SingaporeSingaporeSingapore
  5. 5.Genome Institute of SingaporeSingaporeSingapore

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