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An Exact and Polynomial Distance-Based Algorithm to Reconstruct Single Copy Tandem Duplication Trees

  • Olivier Elemento
  • Olivier Gascuel
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2676)

Abstract

The problem of reconstructing the duplication tree of a set of tandemly repeated sequences which are supposed to have arisen by unequal recombination, was first introduced by Fitch (1977), and has recently received a lot of attention. In this paper, we deal with the restricted problem of reconstructing single copy duplication trees. We describe an exact and polynomial distance based algorithm for solving this problem, the parsimony version of which has previously been shown to be NP-hard (like most evolutionary tree reconstruction problems). This algorithm is based on the minimum evolution principle, and thus involves selecting the shortest tree as being the correct duplication tree. After presenting the underlying mathematical concepts behind the minimum evolution principle, and some of its benefits (such as consistency), we provide a new recurrence equation to estimate the tree length using ordinary least-squares, given a matrix of pairwise distances between the copies. We then show how this equation naturally forms the dynamic programming framework on which our algorithm is based, and provide an implementation in O(n 3) time and O(n 2) space, where n is the number of copies.

Keywords

Branch Length Recurrence Equation Dynamic Programming Algorithm Adjacent Interval Total Time Complexity 
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

  • Olivier Elemento
    • 1
    • 2
    • 3
  • Olivier Gascuel
    • 1
  1. 1.Département d’Informatique Fondamentale et ApplicationsLIRMMMontpellierFrance
  2. 2.IMGT, the international ImMunoGeneTics databaseFrance
  3. 3.Laboratoire d’Immunogénétique Moléculaire, LIGMUniversité Montpellier II, UPR CNRS 1142, IGHMontpellier Cedex 5France

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