- a -

• AASequence() : seq::AASequence
• aaSequence() : seq::CodingSequence
• allAASequences() : seq::CodingSequence
• AminoAcid() : seq::AminoAcid
• asString() : seq::NTSequence, seq::AASequence

- c -

• changeNucleotide() : seq::CodingSequence
• CodingSequence() : seq::CodingSequence

- d -

• description() : seq::NTSequence, seq::AASequence

- f -

• from() : seq::Mutation< Char >
• fromRep() : seq::Nucleotide, seq::AminoAcid

- g -

• getMu() : seq::NucleotideSubstitutionModel

- i -

• intRep() : seq::Nucleotide, seq::AminoAcid
• isAmbiguity() : seq::Nucleotide
• isSynonymousMutation() : seq::CodingSequence
• isValid() : seq::Mutation< Char >

- m -

• message() : seq::ParseException
• Mutation() : seq::Mutation< Char >

- n -

• name() : seq::NTSequence, seq::AASequence
• nonAmbiguousNucleotides() : seq::Nucleotide
• nonAmbiguousSequences() : seq::NTSequence
• NTSequence() : seq::NTSequence
• ntSequence() : seq::CodingSequence
• Nucleotide() : seq::Nucleotide
• NucleotideSubstitutionModel() : seq::NucleotideSubstitutionModel

- o -

• operator!=() : seq::Nucleotide, seq::AminoAcid
• operator<() : seq::Nucleotide, seq::Mutation< Char >, seq::AminoAcid
• operator==() : seq::Nucleotide, seq::Mutation< Char >, seq::AminoAcid

- p -

• ParseException() : seq::ParseException
• pos() : seq::Mutation< Char >
• print() : seq::NucleotideSubstitutionModel

- r -

• reverse() : seq::Mutation< Char >

- s -

• sampleAmbiguities() : seq::NTSequence
• sampleAmbiguity() : seq::Nucleotide
• setDescription() : seq::NTSequence, seq::AASequence
• setName() : seq::NTSequence, seq::AASequence

- t -

• tla() : seq::AminoAcid
• to() : seq::Mutation< Char >
• toChar() : seq::Nucleotide, seq::AminoAcid
• translate() : seq::Codon, seq::AASequence
• translateAll() : seq::Codon

- u -

• updateAASequence() : seq::CodingSequence

- w -

• whatIfMutation() : seq::CodingSequence

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