Abstract: A computational method and system for the comparison and analysis of different objects of information within a database or collection. All objects are compared in a pair-wise fashion so the relative similarity between each object to every other object in the collection is known. A generalized alignment-free method is described for comparing whole genome (coding and non-coding) DNA sequences is used to investigate the relationship among placental mammalian genomes. Differences in word feature frequency profiles (FFP) are used to derive distance and infer evolutionary relationships.