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