Prokaryote Systematics: The Evolution of a Science: "Two main types of analysis are used today to infer phylogenetic trees from sequence alignments, evolutionary distance analysis (Fitch and Margoliash, 1967; Felsenstein, 1982) and maximum parsimony analysis (Fitch, 1971; Felsenstein, 1982). The former takes into account only the number of positions that differ in composition between pairs of sequences - this pair-wise difference being formally a distance. The latter looks at the quality of the difference between sequences, i.e., at which positions have different compositions in different sequences and the nature of these differences. Evolutionary distance analysis uses less of the information in an alignment than does maximum parsimony analysis. A crude analogy that to some extent captures the distinction between the two is that of a person arriving at a city from some far-away place, having traveled by some arbitrarily chosen circuitous route. A distance measurement would concern itself only with how far the person has traveled, not the route, the travel time or where the traveler began. A parsimony analysis attempts to reconstruct the actual route taken."