| Name | Description | Type | Package | Framework |
| AmbiguityDNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| AmbiguityDNARNAHybridCompoundSet | Ambiguity set for hybrid DNA/RNA sequences. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AmbiguityRNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| AminoAcidCompound | Used to describe an Amino Acid. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| AminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.core.sequence.compound | BioJava |
| CodonCompound | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| DNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| NucleotideCompound | Class | org.biojava.nbio.core.sequence.compound | BioJava | |
| RNACompoundSet | Class | org.biojava.nbio.core.sequence.compound | BioJava | |