Local Search for the Maximum Parsimony Problem

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.

• Type: Conference
• Year: 2005
• Where: ICNC
• Authors: Adrien Goëffon, Jean-Michel Richer, Jin-Kao Hao
• Keywords: ICNC 2005, Maximum Parsimony Criterion, Phylogenetic Tree Reconstruction, Subtree Swapping Neighborhood