A distance-based information preservation tree crossover for the maximum parsimony problem

Authors:
Adrien Goëffon;Jean-Michel Richer;Jin-Kao Hao
Affiliations:
LERIA, University of Angers, Angers, France;LERIA, University of Angers, Angers, France;LERIA, University of Angers, Angers, France
Venue:
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Year:
2006

Citing 3
Cited 1

Inferring Phylogenetic Trees Using Evolutionary Algorithms

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Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem

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Local search for the maximum parsimony problem

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Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem

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Abstract

The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of evolutionary changes. Known to be NP-complete, the MP problem has many applications. This paper introduces a Distance-based Information Preservation (DiBIP) Tree Crossover. Contrary to previous crossover operators, DiBIP uses a distance measure to characterize the semantic information of a phylogenetic tree and ensures the preservation of distance related properties between parents and offspring. The performance of DiBIP is assessed with a mimetic algorithm on a set of 28 benchmark instances from the literature. Comparisons with 3 state-of-the-art algorithms show very competitive results of the proposed approach with improvement of some previously best results found.