Heuristic Methods for Phylogenetic Reconstruction with Maximum Parsimony

Maximum Parsimony (MP) is a character-based approach that relies on the work of the german entomologist Willy Hennig (1913-1976). Although Hennig’s work has generated significant controversy, the principles that underlie what was later called cladistics, laid the basis for a convenient and powerful method for the analysis of molecular data with the use of computers. For more details about the history of MP see [9] (p. 136). Cladistics also referred as phylogenetic systematics can be viewed as a philosophy of classification that arranges organisms only by their order of branching in an evolutionary tree. The leaves of the tree are labelled with the OTUs (Operational Taxonomic Unit) of the problem. Ideally, the trees (or cladograms) that