Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks

  • Tetsuo Asano
  • Jesper Jansson
  • Kunihiko Sadakane
  • Ryuhei Uehara
  • Gabriel Valiente
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6129)


The Robinson-Foulds distance, which is the most widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two networks N 1,N 2 with n leaves, m nodes, and e edges, the Robinson-Foulds distance measures the number of clusters of descendant leaves that are not shared by N 1 and N 2. The fastest known algorithm for computing the Robinson-Foulds distance between those networks runs in O(m(m + e)) time. In this paper, we improve the time complexity to O(n(m + e)/logn) for general networks and O(n m/logn) for general networks with bounded degree, and to optimal O(m + e) time for planar phylogenetic networks and bounded-level phylogenetic networks. We also introduce the natural concept of the minimum spread of a phylogenetic network and show how the running time of our new algorithm depends on this parameter. As an example, we prove that the minimum spread of a level-k phylogenetic network is at most k + 1, which implies that for two level-k phylogenetic networks, our algorithm runs in O((k + 1)(m + e)) time.


Characteristic Vector Internal Node Faster Computation Outer Face Phylogenetic Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Tetsuo Asano
    • 1
  • Jesper Jansson
    • 2
  • Kunihiko Sadakane
    • 3
  • Ryuhei Uehara
    • 1
  • Gabriel Valiente
    • 4
  1. 1.School of Information ScienceJapan Advanced Institute of Science and TechnologyIshikawaJapan
  2. 2.Ochanomizu UniversityTokyoJapan
  3. 3.National Institute of InformaticsTokyoJapan
  4. 4.Algorithms, Bioinformatics, Complexity and Formal Methods Research GroupTechnical University of CataloniaBarcelonaSpain

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