Purpose: This tool highlights matches, mismatches, transition and transversion mutations, and silent and non-silent mutations. The nucleotide sequences must be aligned and in frame. This tool is particularly useful for visualizing potential recombination and hypermutation in closely related sequences, such as those isolated from a single patient.
Details: If the "Change Masters" button is not clicked, the first sequence in the file will be taken as the master sequence. In the case of multiple master sequences, the top n will be used. For descriptions of options and output, see Highlighter Explanation.