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.
- GapPenalty->p specifies that the similarity of sequences should have an amount p subtracted for every run of insertions or deletions needed to align the sequences.
Basic Examples (2)
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: