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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
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