| Name | Description | Type | Package | Framework |
| AligMatEl | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| AlignTools | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| GapArray | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| IdxComparator | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| IndexPair | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| JointFragments | A utility class that defines which set of atoms are considered to be on equivalent positions. | Class | org.biojava.nbio.structure.align.helper | BioJava |