Purpose: To document the nature and context of nucleotide substitutions in a sequence population relative to a reference sequence. See details below. For a simple "quick and dirty" scan for hypermutants, try the QC Tool.
Details: The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. Please choose the reference sequence carefully. For example, for an intrapatient set, the reference should probably be the most common form in the first sampled time point; for a set of unrelated sequences, the reference should probably be the consensus sequence for the appropriate subtype. Before using, please read: