HADAMARD CONJUGATION - A VERSATILE TOOL FOR MODELING NUCLEOTIDE-SEQUENCE EVOLUTION

Hadamard conjugation has proved to be a useful tool in examining some of the properties of the patterns of nucleotide sequences arising from the evolution of the taxa they represent. It has a considerable advan tage in that the formulae are independent of the phylogenetic structur e under consideration, and can be given for any number of taxa. Hadama rd conjugation is outlined and four applications are introduced. The a pplications are the theoretical examination of tree building methods, the generation of sample sequences under various models for simulation studies, the identification of some phylogenetic invariants, and the closest tree method for inferring phylogenetic trees and their edge le ngths.