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
