In spite of all the uncertainty, it is possible to know , for certain, that all of the rules for inferring homology do have exceptions. This is proven by character conflict, in which there is no single tree which is consistent with all the evidence, and in which different rules for inference yield different best trees. Assert the overriding correctness of parsimony. Of these four, assertion of parsimony is chosen by many contemporary cladists. Unfortunately, such definite answers may well be wrong.
Suspension of judgment is usually a sound choice, but deeply unsatisfying.
Molecular sequences are becoming increasingly important in phylogenetic inference, and they have distinct properties. The logic of phylogenetic inference is identical for molecular and morphological characters. Molecular characters are available in vast numbers. Every amino acid in every protein is a character. Similarly, every base-pair in every gene is a character.