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:

Introduced in 2008