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Next: Step 4 Up: Near Optimal Multiple Sequence Previous: Step 2

Step 3

Again, only those gaps of ak are inserted into tk and tk+1 that are not already present in tk. Since each gap of sequence ak that is considered is inserted into both, tk and tk+1, the score of this alignment is still optimal, as gap against gap scores zero. In Figure 9 the down arrows correspond to this step. The dark rectangles represent the inserted gaps. After those two steps the partial score of the MSA and the score between sequences ak and ak+1 are both still optimal.

Chantal Korostensky