title: The worst case complexity of maximum parsimony.
abstract: One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.
authors.affiliation: Department of Computer Science, Ben-Gurion University of the Negev , Beer Sheva, Israel .
authors.forename: Amir
authors.initials: A
authors.lastname: Carmel
authors.forename: Noa
authors.initials: N
authors.lastname: Musa-Lempel
authors.forename: Dekel
authors.initials: D
authors.lastname: Tsur
authors.forename: Michal
authors.initials: M
authors.lastname: Ziv-Ukelson
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D015233:Models, Statistical; D010802:Phylogeny
keywords: asymmetric scoring matrix; dendograms; large parsimony; maximum parsimony; phylogenetic reconstruction; phylogeny