Theory and Practice of Ultra-Perfection

Abstract Perfection has been used as a criteria to classify rearrangement scenarios since 2004. However, there is a fundamental bias towards extant species in the original definition: ancestral species are not bound to perfection. Here we develop a new theory of perfection that takes an egalitarian view of species, and we examine the fitness of this theory on several datasets. Supplementary Material is available at www.liebertonline.com/cmb.