Maximum Parsimony Advances for Native Phylogenetic Stemmatics

Abstract

Our ultimate aim is to design an algorithm that generates the most parsimonious tree where extant texts may be ancestors of other texts. The algorithm accepts a set of extant manuscripts or a multiple alignment of such texts. The algorithm examines all most parsimonious (MP) trees generated by conventional phylogenetic methods and attempts to promote leaves to internal nodes while maintaining parsimony. The algorithm outputs the most compact parsimonious tree possible by checking all possible sequences of promotions.