The Needleman-Wunsch and Smith-Waterman algorithms are two algorithms that are very famous and are still widely used when performing sequence alignment. The former is used for performing a global aligment, while the latter is used to perform local alignements. Below is a table that holds their specific differences.
| Needleman-Wunsch algorithm | Smith-Waterman algorithm | |
|---|---|---|
| Initialization | First row and first column are subject to gap penalty | First row and first column are set to 0 |
| Scoring | Score can be negative | Negative score is set to 0 |
| Traceback | Begin with the cell at the lower right of the matrix, end at top left cell | Begin with the highest score, end when 0 is encountered |