Algorithms in Bioinformatics

Volume 3692 of the series Lecture Notes in Computer Science pp 239-250

Minimum Recombination Histories by Branch and Bound

  • Rune B. LyngsøAffiliated withDept. of Statistics, Oxford University
  • , Yun S. SongAffiliated withDept. of Computer Science, University of California
  • , Jotun HeinAffiliated withDept. of Statistics, Oxford University

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Recombination plays an important role in creating genetic diversity within species, and inferring past recombination events is central to many problems in genetics. Given a set M of sampled sequences, finding an evolutionary history for M with the minimum number of recombination events is a computationally very challenging problem. In this paper, we present a novel branch and bound algorithm for tackling that problem. Our method is shown to be far more efficient than the only preexisting exact method, described in [1]. Our software implementing the algorithm discussed in this paper is publicly available.