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 |