Classification and biogeography should be informed by reliable phylogenetic reconstruction. This may be recovered from the mainly speculative literature by a nine-step protocol of critical methods, the “operative transform.” Piecemeal total evidence is attained by combining separately published support values for the same branch arrangement with Bayes' Formula. Joint probability correction is advanced for multiple test problems of conclusions of monophyly necessarily regarded as sets. Tables are given for conversion of nonparametric bootstrap values and decay indexes into probabilities, based on four-taxon simulations. Uncontested morphology-based branch arrangements are assigned high priors. Probabilities associated with unaccounted assumptions are addressed by a general correction factor. A probabilistic calculation allows the inference of two or more reliable internodes from a series of less well-supported internodes. A patristic distance of at least two internodes is used to support inference from molecular data alone of an intermediate lineage for recognition of supraspecific segregate taxonomic entities. Recognizing paraphyletic taxa when appropriate preserves attributes of inferred functional evolution providing taxic unity and value. Evolutionary Lazarus taxa contravening Dollo's Rule against re-evolution of complex traits justify interpretations of reticulation. This method of evaluation of the decisiveness of published molecular studies is exemplified with previously published cladograms focused on Malpighiales and the moss family Pottiaceae. Additional consideration of evolutionary process not reflected in phylogenetic analysis leads to reliable hypotheses of evolutionary relationship.