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Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction

Author

Listed:
  • Jacek Blazewicz
  • Piotr Formanowicz
  • Pawel Kedziora
  • Pawel Marciniak
  • Przemyslaw Taront

Abstract

One of the most important aspect of molecular and computational biology is the reconstruction of evolutionary relationships. The area is well explored after decades of intensive research. Despite this fact there remains a need for good and efficient algorithms that are capable of reconstructing the evolutionary relationship in reasonable time. Since the problem is computationally intractable, exact algorithms are used only for small groups of species. In the Maximum Parsimony approach the time of computation grows so fast when number of sequences increases, that in practice it is possible to find the optimal solution for instances containing about 20 sequences only. It is this reason that in practical applications, heuristic methods are used. In this paper, parallel adaptive memory programming algorithms based on Maximum Parsimony and some known neighborhood search methods for phylogenetic tree construction are proposed, and the results of computational experiments are presented. The proposed algorithms achieve a superlinear speedup and find solutions of good quality. Copyright The Author(s) 2011

Suggested Citation

  • Jacek Blazewicz & Piotr Formanowicz & Pawel Kedziora & Pawel Marciniak & Przemyslaw Taront, 2011. "Adaptive memory programming: local search parallel algorithms for phylogenetic tree construction," Annals of Operations Research, Springer, vol. 183(1), pages 75-94, March.
    • Handle: RePEc:spr:annopr:v:183:y:2011:i:1:p:75-94:10.1007/s10479-010-0682-5
    DOI: 10.1007/s10479-010-0682-5
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    References listed on IDEAS

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    1. Lin, Yu-Min & Fang, Shu-Cherng & Thorne, Jeffrey L., 2007. "A tabu search algorithm for maximum parsimony phylogeny inference," European Journal of Operational Research, Elsevier, vol. 176(3), pages 1908-1917, February.
    2. Taillard, Eric D. & Gambardella, Luca M. & Gendreau, Michel & Potvin, Jean-Yves, 2001. "Adaptive memory programming: A unified view of metaheuristics," European Journal of Operational Research, Elsevier, vol. 135(1), pages 1-16, November.
    3. Fred Glover, 1989. "Tabu Search---Part I," INFORMS Journal on Computing, INFORMS, vol. 1(3), pages 190-206, August.
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