Single data sets, whether derived from morphological or molecular evidence, provide one-off estimates of the correct phylogeny. Their reliability can only be gauged by statistical approaches such as bootstrapping or clade decay, but these test only whether there are sufficient characters in the data matrix to justify the groupings identified. They do not test whether the characters themselves are reliable. Consequently, confidence in the correctness of phylogenetic interpretations comes primarily from discovering the same (or statistically indistinguishable) patterns from independent data sets.
Congruence studies are most advanced for echinoids, where four independent data sets (two morphological and two molecular) provide strong corroboration for a single phylogenetic scheme. Analysis of all four data sets combined generates a highly robust hypothesis of relationships. The situation is very different for asteroids. Two analyses based on morphological data have reached very different conclusions. Three independent molecular data sets also have been compiled, but none has a statistically reliable signal concerning higher taxon relationships. Even combining all three molecular data sets fails to generate a statistically robust solution, implying that the major lines of asteroids diverged rapidly from one another. For ophiuroids, both morphological and molecular data generate topologies that for the most part lack statistical robustness. There is currently no cladistic analysis of holothurian relationships based on morphological data, and only a few taxa have been sequenced. The molecular data is, however, congruent and does permit an initial assessment of relationships. Nothing definite can be deduced about crinoid relationships since even fewer molecular sequences are known and morphological analysis remains sketchy.
Class-level relationships derived from two morphological and two molecular data sets also show considerable congruence, though a single definitive solution has yet to emerge.