| Name | Description | Type | Package | Framework |
| AFPCalculator | a class that performs calculations on AFPCHainsAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPChainer | a class to chain AFPs to an alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPOptimizer | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| AFPPostProcessor | does post processing after alignment chainginAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| FatCatAligner | A class that does calculations on an AFPChainAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| FatCatParameters | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| FCAlignHelper | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| SigEva | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| StructureAlignmentOptimizer | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |