- _ -

• __attribute__() : Sequence

- a -

• all_missing() : Sequence
• allele_counts() : Sequence

- c -

• calcHKA() : Sequence
• calculate_scales() : Sequence::coalsim
• coalesce() : Sequence::coalsim
• ConditionalTraj() : Sequence::coalsim
• ConditionalTrajNeutral() : Sequence::coalsim
• containsCharacter() : Sequence
• crossover() : Sequence::coalsim

- d -

• difference_matrix() : Sequence
• Different() : Sequence
• diffType() : Sequence
• diffTypeMulti() : Sequence
• Disequilibrium() : Sequence::Recombination
• diversity_from_counts() : Sequence

- f -

• faywuh() : Sequence
• from_msformat() : Sequence

- g -

• Gapped() : Sequence::Alignment , Sequence
• garud_statistics() : Sequence
• get_all_descendants() : Sequence::coalsim
• get_ColView() : Sequence
• get_ConstColView() : Sequence
• get_ConstRowView() : Sequence
• get_RowView() : Sequence

- h -

• haplotype_diversity() : Sequence
• hprime() : Sequence
• HudsonsC() : Sequence::Recombination

- i -

• init_marginal() : Sequence::coalsim
• init_sample() : Sequence::coalsim
• integrate_genetic_map() : Sequence::coalsim
• Intermediates2() : Sequence
• Intermediates3() : Sequence
• internalGapCheck() : Sequence
• is_descendant() : Sequence::coalsim
• is_different_matrix() : Sequence
• IsAlignment() : Sequence::Alignment
• isDNA() : Sequence
• isseg() : Sequence::coalsim

- l -

• label_haplotypes() : Sequence

- m -

• make_polySiteVector() : Sequence
• make_slice() : Sequence
• make_window() : Sequence
• makeCodonUsageTable() : Sequence
• makeCountList() : Sequence
• mean() : Sequence
• meanAndVar() : Sequence
• minimize_arg() : Sequence::coalsim
• mutsShortestPath() : Sequence

- n -

• nbiallelic_sites() : Sequence
• neutral_sample() : Sequence::coalsim
• non_reference_allele_counts() : Sequence
• NotAGap() : Sequence
• nSL() : Sequence
• nsl() : Sequence
• number_of_haplotypes() : Sequence
• NumDiffs() : Sequence
• nvariable_sites() : Sequence

- o -

• operator+() : Sequence
• operator++() : Sequence
• operator+=() : Sequence
• operator-() : Sequence
• operator--() : Sequence
• operator-=() : Sequence
• operator<<() : Sequence::coalsim , Sequence
• operator>>() : Sequence::coalsim , Sequence
• output_gametes() : Sequence::coalsim

- p -

• PairwiseLD() : Sequence::Recombination
• pick_branch() : Sequence::coalsim
• pick_uniform_spot() : Sequence::coalsim
• polyTableValid() : Sequence
• process_variable_sites() : Sequence

- r -

• RemoveGaps() : Sequence::Alignment
• RemoveTerminalGaps() : Sequence::Alignment
• rescale_arg() : Sequence::coalsim
• rescale_mutation_positions() : Sequence::coalsim
• rmin() : Sequence
• rotatePolyTable() : Sequence

- s -

• sample_length() : Sequence::coalsim
• Snn_statistic() : Sequence

- t -

• tajd() : Sequence
• thetah() : Sequence
• thetal() : Sequence
• thetapi() : Sequence
• thetaw() : Sequence
• to_msformat() : Sequence
• total_length() : Sequence::coalsim
• total_number_of_mutations() : Sequence
• total_time() : Sequence::coalsim
• total_time_on_arg() : Sequence::coalsim
• Translate() : Sequence
• Trim() : Sequence::Alignment
• TrimComplement() : Sequence::Alignment
• TsTv() : Sequence

- u -

• UnGappedLength() : Sequence::Alignment

- v -

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