Some people use GapShow with this option to see the differences between very similar sequences. And here is the corresponding graphic output . Gap uses the algorithm of Needleman and Wunsch to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman.
Figure makes figures and posters by drawing graphics and text together.
You can include output from other GCG graphics programs as part of a figure. PileUp creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. LineUp is a screen editor for editing multiple sequence alignments. You can edit up to 30 sequences simultaneously.