1. BestFit:
Make
an optimal alignment of the best segment of similarity between two sequences by inserting gaps to
maximize the number of matches using the local
homology algorithm of Smith and
Waterman.
2. Compare:
Compare two protein or nucleic
acid sequences
3. DotPlot:
Make a dot-plot with the output
file from Compare.
4. Gap:
Alignment
of two sequences which has maximum base matches and minimum gap by using the algorithm of
Needleman and Wunsch.
5. GapShow:
Graphic of alignment (use Gap or Bestfit first)
6. FrameAlign:
Create
an optimal alignment between a protein sequence and the codons in 3 reading frames on a nucleotide
sequence
7. ProfileGap:
Make an optimal alignment between
a profile and one or more sequences
Pairwise Comparsion
