A morphological phylogenetic analysis of the coral families Oculinidae and Meandrinidae suggest multiple transitions between colonial and solitary forms. Many morphological characters are logically dependent on a taxon being colonial. The treatment of not applicable characters has remained unresolved, with traditional treatments of not applicable characters having well known flaws. A new method for treating not applicable characters, the Not Applicable Corrected Tree Length (NACTL) method, is presented. The NACTL method retrieves a different phylogenetic signal than traditional approaches, but is more consistent with molecular phylogenetic analyses.