Overlap over;
over.setOverlap(alignment, lA, lB, 0); // Fix gaps at the beginning and end of the sequences
traceBack(); // Traceback the alignment to populate seqAaln and seqBaln
Overlap over;
over.setOverlap(alignment, lA, lB, 0); // Fix gaps at the beginning and end of the sequences
traceBack(); // Traceback the alignment to populate seqAaln and seqBaln