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The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches

  • Mukul S. Bansal
  • Oliver Eulenstein
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene duplication events. This problem is NP-complete and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. A classical local search problem is the \(\mathop{\rm NNI}\) search problem, which is based on the nearest neighbor interchange operation. In this work we (i) provide a novel near-linear time algorithm for the \(\mathop{\rm NNI}\) search problem, (ii) introduce extensions that significantly enlarge the search space of the \(\mathop{\rm NNI}\) search problem, and (iii) present algorithms for these extended versions that are asymptotically just as efficient as our algorithm for the \(\mathop{\rm NNI}\) search problem. The substantially extended \(\mathop{\rm NNI}\) search problem, along with the exceptional speed-up achieved, make the gene-duplication problem more tractable for large-scale phylogenetic analyses.

Keywords

Species Tree Local Search Gene Duplication Gene Tree Search Problem 
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 2008

Authors and Affiliations

  • Mukul S. Bansal
    • 1
  • Oliver Eulenstein
    • 1
  1. 1.Department of Computer ScienceIowa State UniversityUSA

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