Three-item analysis:: Hierarchical representation and treatment of missing and inapplicable data

Matrix-based methods, including parsimony programs, represent and treat missing data in the same way, such that every character-state is possible, and inapplicable data, such that every character state is impossible. This is because the hierarchical nature of homology assessments cannot be represented in taxon-character matrices. We show that the hierarchical representation of hypotheses of homology used in three-item analysis permits the accurate treatment of missing and inapplicable data.