Heuristics for the Phylogeny Problem

Alexandre Andreatta (andreattuniriotec.br)
Celso Ribeiro (celsoinf.puc-rio.br)

Abstract: A phylogeny is a tree that relates taxonomic units, based on their similarity over a set of characters. The problem of finding a phylogeny with the minimum number of evolutionary steps (the so-called parsimony criterion) is one of the main problems in comparative biology. In this work, we study different heuristic approaches to the phylogeny problem under the parsimony criterion. New algorithms based on metaheuristics are also proposed. All heuristics are implemented and compared under the same framework, leading to consistent and thorough comparative results. Computational results are reported for benchmark instances from the literature.

Keywords: Heuristics, phylogeny, GRASP

Category 1: Applications -- Science and Engineering (Biomedical Applications )

Category 2: Combinatorial Optimization (Meta Heuristics )

Citation: Journal of Heuristics 8 (2002), 429-447.

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Entry Submitted: 10/12/2003
Entry Accepted: 10/12/2003
Entry Last Modified: 10/12/2003

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