Here is a list of all documented namespace members with links to the namespaces they belong to:

- a -

• add_S_inf_sites() : Sequence
• addIdentityChar() : Sequence
• alignment_length() : Sequence
• arg : Sequence

- b -

• basic_dna_alphabet : Sequence
• bottleneck() : Sequence

- c -

• calcHKA() : Sequence
• calculate_scales() : Sequence
• CMAX : Sequence::Recombination
• coalesce() : Sequence
• CodonUsageTable : Sequence
• ConditionalTraj() : Sequence
• ConditionalTraj_details() : Sequence
• ConditionalTrajNeutral() : Sequence
• ConditionalTrajNeutral_details() : Sequence
• containsCharacter() : Sequence
• crossover() : Sequence

- d -

• deletion_distance() : Sequence
• Different() : Sequence
• diffType() : Sequence
• diffTypeMulti() : Sequence
• Disequilibrium() : Sequence::Recombination

- e -

• EmptyVector() : Sequence::Alignment
• exponential_change() : Sequence

- f -

• fillIn() : Sequence
• full_dna_alphabet : Sequence

- g -

• gamete_storage_type : Sequence
• Gapped() : Sequence , Sequence::Alignment , Sequence , Sequence::Alignment
• GeneticCodes : Sequence
• get_all_descendants() : Sequence
• GetData() : Sequence::Alignment

- h -

• HudsonsC() : Sequence::Recombination

- i -

• infinite_sites() : Sequence
• infinite_sites_sim_data() : Sequence
• init_marginal() : Sequence
• init_sample() : Sequence
• insertion_distance() : Sequence
• integrate_genetic_map() : Sequence
• Intermediates2() : Sequence
• Intermediates3() : Sequence
• internalGapCheck() : Sequence
• is_descendant() : Sequence
• IsAlignment() : Sequence::Alignment
• isseg() : Sequence

- m -

• makeCodonUsageTable() : Sequence
• makeCountList() : Sequence
• MAX_SEGS_INC : Sequence
• MAX_SEGSITES : Sequence
• mean() : Sequence
• meanAndVar() : Sequence
• minimize_arg() : Sequence
• mismatches() : Sequence
• Mutations : Sequence
• mutsShortestPath() : Sequence

- n -

• neutral_sample() : Sequence
• ngaps() : Sequence
• NotAGap() : Sequence
• Nucleotides : Sequence
• NumDiffs() : Sequence

- o -

• operator+() : Sequence
• operator+=() : Sequence
• operator<<() : Sequence
• operator>>() : Sequence
• output_gametes() : Sequence

- p -

• pep_alphabet : Sequence
• PermuteCorrelation() : Sequence
• pick2() : Sequence
• pick2_in_deme() : Sequence
• pick_branch() : Sequence
• pick_spot() : Sequence
• pick_uniform_spot() : Sequence
• polymorphicSite : Sequence
• polySiteVector : Sequence
• PolyTableValid() : Sequence
• PRECISION : Sequence::Recombination

- r -

• ReadNObjects() : Sequence::Alignment
• RemoveFixedOutgroupInsertions() : Sequence::Alignment
• RemoveGaps() : Sequence::Alignment , Sequence
• RemoveInvariantColumns() : Sequence
• RemoveTerminalGaps() : Sequence::Alignment
• rescale_arg() : Sequence
• rescale_mutation_positions() : Sequence
• rotatePolyTable() : Sequence

- s -

• sample_length() : Sequence
• SEQMAXDOUBLE : Sequence
• SEQMAXUNSIGNED : Sequence
• Snn_test() : Sequence
• Snn_test_pairwise() : Sequence

- t -

• total_length() : Sequence
• total_time() : Sequence
• total_time_on_arg() : Sequence
• Translate() : Sequence
• Trim() : Sequence::Alignment
• TrimComplement() : Sequence::Alignment
• TsTv() : Sequence

- u -

• UnGappedLength() : Sequence::Alignment

- v -

• validForPolyAnalysis() : Sequence::Alignment
• validSeq() : Sequence
• variance() : Sequence