Method for identifying combinations of motifs that do not mutate simultaneously in a set of viral polypeptide sequences comprising a putative drug binding site

Methods for identifying a motif or a combination of motifs having a Boolean state of predetermined mutations in a set of sequences including a) aligning a set of sequences of ordered motifs represented by a single-character code, b) comparing a reference sequence with the set of sequences aligned in step (a), c) identifying motifs not having mutated simultaneously and/or motifs having mutated simultaneously at least once on at least one sequence of the set and not having mutated on another sequence of the set.