| seq::AASequence | An amino acid sequence |
| seq::AminoAcid | An amino acid |
| seq::CodingSequence | A coding sequence represents a nucleotide sequence that codes for an amino acid sequence (an oligo- or polypeptide) |
| seq::Codon | Utility class that defines the genetic code |
| seq::Mutation< Char > | A mutation in a sequence of type Char |
| seq::NTSequence | A nucleotide sequence |
| seq::Nucleotide | A nucleotide, including support for ambiguity codes |
| seq::NucleotideSubstitutionModel | Describes the mutation behaviour of (the whole of) replication enzymes for one replication cycle |
| seq::ParseException | Exception thrown when an error was encountered while parsing the string representation of an nucleotide, nucleotide sequence, amino acid, amino acid sequence, or a FASTA file |
1.4.4