• Similarity matrix vs distance matrix

The matrix shows the similarity between pairs of sequences, not an evolutionary distance, that is, no correction for multiple base changes at a single position has been applied.

• Alignment

The most similar sequence for the alignment template is found the same way as for the Sequence Match program by looking for the sequence that shares the highest proportion of oligomers of a given length (7-mers) with your sequence. It is NOT determined by making a total similarity matrix and picking the top scores off of that; that would somewhat better but much slower.

In some cases,the alignment could clearly be improved, but the overall performance seems satisfactory.