| Name | Description | Type | Package | Framework |
| AFPChainFlipper | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPChainXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPChainXMLParser | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| HasResultXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| MultipleAlignmentXMLConverter | Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format. | Class | org.biojava.nbio.structure.align.xml | BioJava |
| MultipleAlignmentXMLParser | Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered. | Class | org.biojava.nbio.structure.align.xml | BioJava |
| PdbPairsMessage | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PdbPairXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PositionInQueueXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| RepresentativeXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |