Comparison

Two sequences, one difference list.

Equal lengths get an ungapped identity across the whole molecule. A gapped Needleman–Wunsch alignment, and a Smith–Waterman local alignment with the same scores, are drawn when each sequence is 1,200 bp or shorter. Up to 6 sequences of 400 bp can be aligned progressively. That alignment is not MUSCLE or MAFFT. The tree is neighbor-joining on its p-distance.