Cladistic analysis can be used with molecular or morphological data. In fact the original cladisitc analyses by Willi Henneg were done with morphological characters, before molecular data were used in systematics. The essence of cladistic analysis is an attempt to group organisms on the basis of the evolutionary relationships, not on the basis on similarity. This methods picks a group of organisms to be classified, and then places organisms together which have shared, derived characters. This means that the analysis picks traits of an organism to study (be they morphology or molecules), postulates what the characters looked like in the ancestor, and then uses the principle of parsimony to place together creatures which have in common derived features.

Cladisitic analysis can be contrasted with phenetics.