|
Class Summary |
| Alignment |
Holds the output of a pairwise sequences alignment. |
| Cell |
A cell in a similarity matrix, to hold row, column and score. |
| Directions |
Traceback directions. |
| Markups |
Markups line characters. |
| NeedlemanWunsch |
An implementation of the Needleman-Wunsch algorithm for biological global
pairwise sequence alignment. |
| NeedlemanWunschGotoh |
An implementation of the Needleman-Wunsch algorithm with Gotoh's improvement
for biological global pairwise sequence alignment. |
| Sequence |
A basic (nucleic or protein) sequence. |
| SmithWatermanGotoh |
An implementation of the Smith-Waterman algorithm with Gotoh's improvement
for biological local pairwise sequence alignment. |
| TracebackNode |
Traceback node |