GapPenalty is an option for SequenceAlignment and related functions that gives the additional cost associated with each gap corresponding to a run of insertions or deletions.
By default, an alignment is found with two gaps:
Increasing the penalty for gaps forces another alignment with fewer gaps:
The default alignment score:
Add an additional penalty for the gap:
SimilarityRules SequenceAlignment SmithWatermanSimilarity NeedlemanWunschSimilarity Split