| Name | Description | Type | Package | Framework |
| SmithWaterman3Daligner | provides a 3D superimposition based on the sequence alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.seq | BioJava |
| SmithWaterman3DParameters | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SmithWatermanUserArgumentProcessor | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SmithWatermanUserArgumentProcessor .SmithWatermanStartupParams | Class | org.biojava.nbio.structure.align.seq | BioJava | |