Computing Refined Buneman Trees in Cubic Time

  • Gerth Stølting Brodal
  • Rolf Fagerberg
  • Anna Östlin
  • Christian N. S. Pedersen
  • S. Srinivasa Rao
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)


Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbor joining is a popular distance based tree reconstruction method. It always proposes fully resolved binary trees despite missing evidence in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n 5) and a space consumption of O(n 4). In this paper, we present an algorithm with running time O(n 3) and space consumption O(n 2). The improved complexity of our algorithm makes the method of refined Buneman trees computational competitive to methods based on neighbor joining.


Binary Tree Evolutionary Tree Dissimilarity Measure Space Usage Central Edge 
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 2003

Authors and Affiliations

  • Gerth Stølting Brodal
    • 1
  • Rolf Fagerberg
    • 1
  • Anna Östlin
    • 2
  • Christian N. S. Pedersen
    • 3
  • S. Srinivasa Rao
    • 4
  1. 1.BRICS (Basic Research in Computer Science), Department of Computer ScienceUniversity of AarhusÅrhus CDenmark
  2. 2.IT University of CopenhagenCopenhagen NV.
  3. 3.Bioinformatics Research Center (BiRC), Department of Computer ScienceUniversity of AarhusÅrhus CDenmark
  4. 4.School of Computer ScienceUniversity of WaterlooWaterloo

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