A Novel Method for Economical Diagnosis of Cladograms under Sankoff Optimization
Ward C. Wheeler · Cladistics · 1994
Abstract Abstract —A method is proposed to recode certain phylogenetic cost matrices in order to lessen the computational burden involved in the search for parsimonious cladograms. Multistate characters with complex costs among character states are converted to unordered multistate and binary variables with differential weights. These new variables can be optimized efficiently. The method has applications in cases where character states are distributed hierarchically and symmetrically. Cases of inapplicable states in morphology, and transition-transversion weighting in molecular sequence data are discussed this light.