Journal of Mathematical Biology

, Volume 74, Issue 1–2, pp 239–257 | Cite as

On the fixed parameter tractability of agreement-based phylogenetic distances

  • Magnus Bordewich
  • Celine Scornavacca
  • Nihan Tokac
  • Mathias Weller
Article

Abstract

Three important and related measures for summarizing the dissimilarity in phylogenetic trees are the minimum number of hybridization events required to fit two phylogenetic trees onto a single phylogenetic network (the hybridization number), the (rooted) subtree prune and regraft distance (the rSPR distance) and the tree bisection and reconnection distance (the TBR distance) between two phylogenetic trees. The respective problems of computing these measures are known to be NP-hard, but also fixed-parameter tractable in their respective natural parameters. This means that, while they are hard to compute in general, for cases in which a parameter (here the hybridization number and rSPR/TBR distance, respectively) is small, the problem can be solved efficiently even for large input trees. Here, we present new analyses showing that the use of the “cluster reduction” rule—already defined for the hybridization number and the rSPR distance and introduced here for the TBR distance—can transform any \(O(f(p) \cdot n)\)-time algorithm for any of these problems into an \(O(f(k) \cdot n)\)-time one, where n is the number of leaves of the phylogenetic trees, p is the natural parameter and k is a much stronger (that is, smaller) parameter: the minimum level of a phylogenetic network displaying both trees.

Keywords

Phylogenetic network Hybridization number Cluster reduction SPR distance TBR distance 

Mathematics Subject Classification

05C85 68R10 92-08 05C05 05C60 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Magnus Bordewich
    • 1
  • Celine Scornavacca
    • 2
  • Nihan Tokac
    • 1
  • Mathias Weller
    • 3
  1. 1.School of Engineering and Computing SciencesDurham UniversityDurhamUK
  2. 2.Institut des Sciences de l’EvolutionUniversité de Montpellier, CNRS, IRD, EPHEMontpellier Cedex 5France
  3. 3.Institut de Biologie Computationnelle (IBC), Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM)Université de MontpellierMontpellier Cedex 5France

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