The basic problem in morphological phylogenetics is the assembly of a matrix representing a mapping from each of the taxa being compared to representative measurements for each of the phenotypic characteristics being used as a classifier.
Some phenotypic classifications, particularly those used when analyzing very diverse groups of taxa, are discrete and unambiguous; classifying organisms as possessing or lacking a tail, for example, is straightforward in the majority of cases, as is counting features such as eyes or vertebrae.