SmithWatermanAligner.php
Local pairwise sequence alignment by dynamic programming Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 2 October 2026
Table of Contents
Classes
- SmithWatermanAligner
- The classic Smith-Waterman algorithm : like NeedlemanWunschAligner's matrix, except every cell is floored at zero (a bad-scoring region is simply abandoned instead of dragging the running total negative), the borders start at zero rather than an accumulated gap cost, and the alignment is recovered by walking back from the single highest-scoring cell in the whole matrix - not from the bottom-right corner - stopping as soon as a cell of value zero is reached, rather than at (0, 0).