Local search for the maximum parsimony problem

Authors:
Adrien Goëffon;Jean-Michel Richer;Jin-Kao Hao
Affiliations:
LERIA, University of Angers, Angers Cedex 01, France;LERIA, University of Angers, Angers Cedex 01, France;LERIA, University of Angers, Angers Cedex 01, France
Venue:
ICNC'05 Proceedings of the First international conference on Advances in Natural Computation - Volume Part III
Year:
2005

Citing 2
Cited 2

Heuristics for the Phylogeny Problem

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LVB: parsimony and simulated annealing in the search for phylogenetic trees

Bioinformatics

Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A distance-based information preservation tree crossover for the maximum parsimony problem

PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature

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Abstract

Four local search algorithms are investigated for the phylogenetic tree reconstruction problem under the Maximum Parsimony criterion. A new subtree swapping neighborhood is introduced and studied in combination with an effective array-based tree representation. Computational results are shown on a set of randomly generated benchmark instances as well as on 8 real problems (sequences of phytopathogen γ-proteobacteria) and compared with two references from the literature.