Python/Java Smith Waterman algorithm for string alignment (generic).
Java implementation with advanced tools specific to DNA alignments.
SmithWaterman.py Calculates string alignments; blind to DNA code
Running this program demonstrates the library functionality
smithwatermanalignmnet (Java)
SmithWaterman.java Calculates string alignments; blind to DNA code. A port of above code.
SmithWatermanAdvanced.java Aligns DNA concientiously according to DNA character set definition, which includes wildcards
DNAcodes.java Definition of DNA coding and character equivalency\
TableEntry.java Helper Class (a simple struct) to SmithWaterman
PartialAlignment.java Helper Class to SmithWaterman