In many MSAs both situations will arise: gaps are shifted and
In the MSA of Figure , sequence A has two gaps
and sequence B has three gaps. If we
push the gaps together and move them to the same position, we
combine 5 events to one single event. In addition, the resulting
alignment has a better score (the optimal score in this case) and
also makes more sense from a biological point of view.
Here 5 events can be reduced
to one event by shifting and fusing the gaps.