Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z _ __init__() (AdaptivePolarizationPrior method) (AdHocAncestralAnnotation method) (AllFiltration method) (AncestralAlleleAnnotation method) (AncestralBaseStratification method) (Annotation method) (Annotator method) (BaseContextStratification method) (BaseTransitionStratification method) (BiasedGCConversionFiltration method) (ChunkedStratification method) (CodingSequenceFiltration method) (ContigFiltration method) (ContigStratification method) (CpGFiltration method) (DegeneracyAnnotation method) (DegeneracyStratification method) (DeviantOutgroupFiltration method) (ExistingOutgroupFiltration method) (FASTAHandler method) (FileHandler method) (Filterer method) (Filtration method) (GenomePositionDependentStratification method) (GFFHandler method) (JCSubstitutionModel method) (JointSFS method) (JointSpectra method) (K2SubstitutionModel method) (KingmanPolarizationPrior method) (MaskedFiltration method) (MaximumLikelihoodAncestralAnnotation method) (MaximumParsimonyAncestralAnnotation method) (NoFiltration method) (NoTypeException method) (Parser method) (PolarizationPrior method) (PolyAllelicFiltration method) (RandomStratification method) (Site method) (SiteConfig method) (SiteInfo method) (SnpEffStratification method) (SNPFiltration method) (SNPStratification method) (SNVFiltration method) (Spectra method) (Spectrum method) (Stratification method) (SubstitutionModel method) (SynonymyAnnotation method) (SynonymyStratification method) (TargetSiteCounter method) (TransitionTransversionStratification method) (TskitVariantReader method) (TskitVariantWriter method) (TwoLocusSFS method) (TwoSFS method) (TwoSpectra method) (Variant method) (VCFHandler method) (VCFVariantWriter method) (VEPStratification method) (ZarrVariantReader method) (ZarrVariantWriter method) A AbstractSpectra (class in sfsutils.spectrum) AbstractSpectrum (class in sfsutils.spectrum) AdaptivePolarizationPrior (class in sfsutils.annotation) add_info_to_header() (TskitVariantReader method) (VariantReader method) (ZarrVariantReader method) add_note() (NoTypeException method) AdHocAncestralAnnotation (class in sfsutils.annotation) adjust_target_sites (MaximumLikelihoodAncestralAnnotation attribute) aliases (Annotator attribute) (BaseContextStratification attribute) (FASTAHandler attribute) (FileHandler attribute) (Filterer attribute) (GFFHandler attribute) (Parser attribute) (VCFHandler attribute) all (AbstractSpectra property) (JointSpectra property) (Spectra property) (TwoSpectra property) allele_indices (Site attribute) (Variant attribute) AllFiltration (class in sfsutils.filtration) allow_divergence (AdaptivePolarizationPrior attribute) (KingmanPolarizationPrior attribute) (PolarizationPrior attribute) ALT (Site attribute) (Variant attribute) AncestralAlleleAnnotation (class in sfsutils.annotation) AncestralBaseStratification (class in sfsutils.parser) annotate() (Annotator method) annotate_site() (AdHocAncestralAnnotation method) (AncestralAlleleAnnotation method) (Annotation method) (DegeneracyAnnotation method) (MaximumLikelihoodAncestralAnnotation method) (MaximumParsimonyAncestralAnnotation method) (SynonymyAnnotation method) Annotation (class in sfsutils.annotation) annotations (Annotator attribute) (Parser attribute) Annotator (class in sfsutils.annotation) args (NoTypeException attribute) B BaseContextStratification (class in sfsutils.parser) BaseTransitionStratification (class in sfsutils.parser) BaseType (class in sfsutils.annotation) BiasedGCConversionFiltration (class in sfsutils.filtration) bounds (JCSubstitutionModel attribute) (K2SubstitutionModel attribute) (SubstitutionModel attribute) C cache (Annotator attribute) (BaseContextStratification attribute) (FASTAHandler attribute) (FileHandler attribute) (Filterer attribute) (GFFHandler attribute) (Parser attribute) (VCFHandler attribute) cache() (JCSubstitutionModel method) (K2SubstitutionModel method) (SubstitutionModel method) cd (CodingSequenceFiltration attribute) CHROM (Site attribute) (Variant attribute) chunk_sizes (ChunkedStratification attribute) ChunkedStratification (class in sfsutils.parser) close() (TskitVariantReader method) (TskitVariantWriter method) (VariantReader method) (VariantWriter method) (VCFVariantWriter method) (ZarrVariantReader method) (ZarrVariantWriter method) CodingSequenceFiltration (class in sfsutils.filtration) combine() (Spectra method) confidence_threshold (MaximumLikelihoodAncestralAnnotation attribute) configs (MaximumLikelihoodAncestralAnnotation attribute) contig (BaseContextStratification attribute) contig_lengths (Annotator property) (Filterer property) (Parser property) (TskitVariantReader property) (VariantReader property) (VCFHandler property) (ZarrVariantReader property) ContigFiltration (class in sfsutils.filtration) contigs (ContigFiltration attribute) (ContigStratification attribute) ContigStratification (class in sfsutils.parser) copy() (AbstractSpectrum method) (JointSFS method) (Spectra method) (Spectrum method) (TwoLocusSFS method) (TwoSFS method) corr() (TwoLocusSFS method) (TwoSFS method) count() (TargetSiteCounter method) count_sites() (Annotator method) (Filterer method) (Parser method) (TskitVariantReader method) (VariantReader method) (VCFHandler method) (ZarrVariantReader method) count_target_sites() (AdHocAncestralAnnotation static method) (AncestralAlleleAnnotation static method) (Annotation static method) (DegeneracyAnnotation static method) (MaximumLikelihoodAncestralAnnotation static method) (MaximumParsimonyAncestralAnnotation static method) (SynonymyAnnotation static method) counter (ChunkedStratification attribute) cov() (TwoLocusSFS method) (TwoSFS method) CpGFiltration (class in sfsutils.filtration) D d (Parser attribute) data (AbstractSpectrum attribute) (JointSFS attribute) (JointSpectra attribute) (Spectrum attribute) (TwoLocusSFS attribute) (TwoSFS attribute) (TwoSpectra attribute) DegeneracyAnnotation (class in sfsutils.annotation) DegeneracyStratification (class in sfsutils.parser) DeviantOutgroupFiltration (class in sfsutils.filtration) disable_pbar (Settings attribute) download_file() (Annotator class method) (BaseContextStratification class method) (FASTAHandler class method) (FileHandler class method) (Filterer class method) (GFFHandler class method) (Parser class method) (VCFHandler class method) download_if_url() (Annotator method) (BaseContextStratification method) (FASTAHandler method) (FileHandler method) (Filterer method) (GFFHandler method) (Parser method) (VCFHandler method) drop_empty() (Spectra method) drop_sparse() (Spectra method) drop_zero_entries() (Spectra method) E errors (DegeneracyAnnotation attribute) (SynonymyAnnotation attribute) evaluate_likelihood() (MaximumLikelihoodAncestralAnnotation method) exclude (AdHocAncestralAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) exclude_samples (MaskedFiltration attribute) (Parser attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) ExistingOutgroupFiltration (class in sfsutils.filtration) F fasta (Annotator attribute) (BaseContextStratification attribute) (FASTAHandler attribute) (Filterer attribute) (Parser attribute) FASTAHandler (class in sfsutils.io_handlers) FileHandler (class in sfsutils.io_handlers) fill_monomorphic() (TwoLocusSFS method) (TwoSFS method) filter() (Filterer method) filter_site() (AllFiltration method) (BiasedGCConversionFiltration method) (CodingSequenceFiltration method) (ContigFiltration method) (CpGFiltration method) (DeviantOutgroupFiltration method) (ExistingOutgroupFiltration method) (Filtration method) (MaskedFiltration method) (NoFiltration method) (PolyAllelicFiltration method) (SNPFiltration method) (SNVFiltration method) Filterer (class in sfsutils.filtration) Filtration (class in sfsutils.filtration) filtrations (Filterer attribute) (Parser attribute) first_node_ancestral (SiteInfo attribute) fix_transition_transversion_ratio (K2SubstitutionModel attribute) fixed_params (JCSubstitutionModel attribute) (K2SubstitutionModel attribute) (SubstitutionModel attribute) fold() (JointSFS method) (Spectra method) (Spectrum method) (TwoLocusSFS method) (TwoSFS method) fpmi() (TwoLocusSFS method) (TwoSFS method) from_data() (MaximumLikelihoodAncestralAnnotation class method) from_dataframe() (MaximumLikelihoodAncestralAnnotation class method) (Spectra static method) from_dict() (Spectra static method) from_est_sfs() (MaximumLikelihoodAncestralAnnotation class method) from_file() (AbstractSpectrum class method) (JointSFS class method) (JointSpectra class method) (MaximumLikelihoodAncestralAnnotation class method) (Spectra class method) (Spectrum static method) (TwoLocusSFS class method) (TwoSFS class method) (TwoSpectra class method) from_json() (AbstractSpectrum class method) (JointSFS class method) (JointSpectra class method) (MaximumLikelihoodAncestralAnnotation class method) (Spectrum class method) (TwoLocusSFS class method) (TwoSFS class method) (TwoSpectra class method) from_list() (Spectra static method) (Spectrum static method) from_polydfe() (Spectrum static method) from_polymorphic() (Spectrum static method) from_spectra() (Spectra static method) from_spectrum() (Spectra static method) G GenomePositionDependentStratification (class in sfsutils.parser) get_aliases() (Annotator method) (BaseContextStratification method) (FASTAHandler method) (FileHandler method) (Filterer method) (GFFHandler method) (Parser method) (VCFHandler method) get_base_index() (AdHocAncestralAnnotation class method) (MaximumLikelihoodAncestralAnnotation class method) get_base_string() (AdHocAncestralAnnotation static method) (MaximumLikelihoodAncestralAnnotation static method) get_bound() (JCSubstitutionModel method) (K2SubstitutionModel method) get_bounds() (JCSubstitutionModel method) (K2SubstitutionModel method) (SubstitutionModel method) get_contig() (Annotator method) (BaseContextStratification method) (FASTAHandler method) (Filterer method) (Parser method) get_contig_names() (Annotator method) (BaseContextStratification method) (FASTAHandler method) (Filterer method) (Parser method) get_degeneracy (DegeneracyStratification attribute) get_empty() (Spectra method) get_filename() (Annotator static method) (BaseContextStratification static method) (FASTAHandler static method) (FileHandler static method) (Filterer static method) (GFFHandler static method) (Parser static method) (VCFHandler static method) get_folded_spectra() (MaximumLikelihoodAncestralAnnotation method) get_inferred_site_info() (MaximumLikelihoodAncestralAnnotation method) get_max_abs() (TwoLocusSFS method) (TwoSFS method) get_neutral() (Spectrum static method) get_observed_transition_transversion_ratio() (MaximumLikelihoodAncestralAnnotation method) get_outgroup_divergence() (MaximumLikelihoodAncestralAnnotation method) get_p_config() (MaximumLikelihoodAncestralAnnotation class method) get_p_configs() (MaximumLikelihoodAncestralAnnotation class method) get_p_tree() (MaximumLikelihoodAncestralAnnotation static method) get_pbar() (Annotator method) (Filterer method) (Parser method) (VCFHandler method) get_site_info() (MaximumLikelihoodAncestralAnnotation method) get_type() (AncestralBaseStratification method) (BaseContextStratification method) (BaseTransitionStratification method) (ChunkedStratification method) (ContigStratification method) (DegeneracyStratification method) (GenomePositionDependentStratification method) (RandomStratification method) (SnpEffStratification method) (SNPStratification method) (Stratification method) (SynonymyStratification method) (TransitionTransversionStratification method) (VEPStratification method) get_types() (AncestralBaseStratification method) (BaseContextStratification method) (BaseTransitionStratification method) (ChunkedStratification method) (ContigStratification method) (DegeneracyStratification method) (GenomePositionDependentStratification method) (RandomStratification method) (SnpEffStratification method) (SNPStratification method) (Stratification method) (SynonymyStratification method) (TransitionTransversionStratification method) (VEPStratification method) get_x0() (JCSubstitutionModel static method) (K2SubstitutionModel static method) (SubstitutionModel static method) gff (Annotator attribute) (Filterer attribute) (GFFHandler attribute) (Parser attribute) GFFHandler (class in sfsutils.io_handlers) gt_bases (Site attribute) (Variant property) H has_div (Spectra property) (Spectrum property) has_dots() (Spectra method) hash() (Annotator static method) (BaseContextStratification static method) (FASTAHandler static method) (FileHandler static method) (Filterer static method) (GFFHandler static method) (Parser static method) (VCFHandler static method) I include_samples (MaskedFiltration attribute) (Parser attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) infer() (MaximumLikelihoodAncestralAnnotation method) INFO (Site attribute) (Variant attribute) info_ancestral (Annotator attribute) (Filterer attribute) (Parser attribute) (VCFHandler attribute) info_ancestral_prob (Parser attribute) info_tag (SnpEffStratification attribute) (VEPStratification attribute) ingroup_mask (DeviantOutgroupFiltration attribute) ingroups (AdHocAncestralAnnotation attribute) (DeviantOutgroupFiltration attribute) (MaximumLikelihoodAncestralAnnotation attribute) interior() (TwoLocusSFS method) (TwoSFS method) is_deletion (Site attribute) (Variant attribute) is_empty (AbstractSpectra property) (JointSpectra property) (Spectra property) (TwoSpectra property) is_filtered() (Filterer method) is_folded() (JointSFS method) (Spectra method) (Spectrum method) (TwoLocusSFS method) (TwoSFS method) is_indel (Site attribute) (Variant attribute) is_mnp (Site attribute) (Variant attribute) is_monotonic() (MaximumLikelihoodAncestralAnnotation method) is_snp (Site attribute) (Variant attribute) is_sv (Site attribute) (Variant attribute) is_synonymous() (SynonymyAnnotation static method) is_url() (Annotator static method) (BaseContextStratification static method) (FASTAHandler static method) (FileHandler static method) (Filterer static method) (GFFHandler static method) (Parser static method) (VCFHandler static method) J JCSubstitutionModel (class in sfsutils.annotation) JointSFS (class in sfsutils.spectrum) JointSpectra (class in sfsutils.spectrum) K k (Spectra property) K2SubstitutionModel (class in sfsutils.annotation) kingman() (Spectrum static method) KingmanPolarizationPrior (class in sfsutils.annotation) L likelihood (MaximumLikelihoodAncestralAnnotation attribute) likelihoods (MaximumLikelihoodAncestralAnnotation attribute) load_fasta() (Annotator method) (BaseContextStratification method) (FASTAHandler method) (Filterer method) (Parser method) load_vcf() (Annotator method) (Filterer method) (Parser method) (VCFHandler method) M MAJOR (BaseType attribute) major_ancestral (SiteInfo attribute) major_base (SiteConfig attribute) (SiteInfo attribute) marginalize() (JointSFS method) (JointSpectra method) mask_diagonal() (TwoLocusSFS method) (TwoSFS method) mask_upper() (TwoLocusSFS method) (TwoSFS method) MaskedFiltration (class in sfsutils.filtration) max_sampling_attempts_factor (MaximumLikelihoodAncestralAnnotation attribute) max_sites (Annotator attribute) (Filterer attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) (VCFHandler attribute) MaximumLikelihoodAncestralAnnotation (class in sfsutils.annotation) MaximumParsimonyAncestralAnnotation (class in sfsutils.annotation) merge_groups() (Spectra method) MINOR (BaseType attribute) minor_base (SiteConfig attribute) (SiteInfo attribute) misidentify() (Spectrum method) mismatches (DegeneracyAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) (SynonymyAnnotation attribute) model (MaximumLikelihoodAncestralAnnotation attribute) multiplicity (SiteConfig attribute) mutate() (SynonymyAnnotation static method) N n (Parser attribute) (Spectra property) (Spectrum property) (TwoLocusSFS attribute) (TwoSFS attribute) n_aa_prob (Parser attribute) n_annotated (AdHocAncestralAnnotation attribute) (AncestralAlleleAnnotation attribute) (Annotation attribute) (DegeneracyAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) (MaximumParsimonyAncestralAnnotation attribute) (SynonymyAnnotation attribute) n_chunks (ChunkedStratification attribute) n_div (Spectra property) (Spectrum property) n_filtered (AllFiltration attribute) (BiasedGCConversionFiltration attribute) (CodingSequenceFiltration attribute) (ContigFiltration attribute) (CpGFiltration attribute) (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) (Filterer attribute) (Filtration attribute) (MaskedFiltration attribute) (NoFiltration attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) (SNVFiltration attribute) n_flanking (BaseContextStratification attribute) n_ingroups (AdHocAncestralAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) n_major (SiteConfig attribute) (SiteInfo attribute) n_missing (ExistingOutgroupFiltration attribute) n_monomorphic (Spectra property) (Spectrum property) n_no_ancestral (Parser attribute) n_outgroups (AdHocAncestralAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) n_polymorphic (Spectra property) (Spectrum property) n_pops (JointSFS property) (JointSpectra property) n_processed (CodingSequenceFiltration attribute) n_runs (AdaptivePolarizationPrior attribute) (MaximumLikelihoodAncestralAnnotation attribute) n_samples (TargetSiteCounter attribute) n_samples_target_sites (MaximumLikelihoodAncestralAnnotation attribute) n_sites (AbstractSpectrum property) (Annotator property) (Filterer property) (JointSFS property) (MaximumLikelihoodAncestralAnnotation attribute) (Parser property) (Spectra property) (Spectrum property) (TwoLocusSFS property) (TwoSFS property) (VCFHandler property) n_skipped (DegeneracyAnnotation attribute) (Parser attribute) (SynonymyAnnotation attribute) n_snpeff_comparisons (SynonymyAnnotation attribute) n_target_sites (MaximumLikelihoodAncestralAnnotation attribute) (TargetSiteCounter attribute) n_valid (AncestralBaseStratification attribute) (BaseContextStratification attribute) (BaseTransitionStratification attribute) (ChunkedStratification attribute) (ContigStratification attribute) (DegeneracyStratification attribute) (GenomePositionDependentStratification attribute) (RandomStratification attribute) (SnpEffStratification attribute) (SNPStratification attribute) (Stratification attribute) (SynonymyStratification attribute) (TransitionTransversionStratification attribute) (VEPStratification attribute) n_vep_comparisons (SynonymyAnnotation attribute) NoFiltration (class in sfsutils.filtration) normalize() (Spectra method) (Spectrum method) NoTypeException (class in sfsutils.io_handlers) num_bins (RandomStratification attribute) O open() (TskitVariantWriter static method) (VariantWriter static method) (VCFVariantWriter static method) (ZarrVariantWriter static method) outgroup_bases (SiteConfig attribute) (SiteInfo attribute) outgroup_mask (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) outgroups (AdHocAncestralAnnotation attribute) (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) (MaximumLikelihoodAncestralAnnotation attribute) output (Annotator attribute) (Filterer attribute) P p_bases_first_node (SiteInfo attribute) p_bins (MaximumLikelihoodAncestralAnnotation attribute) p_first_node_ancestral (SiteInfo attribute) p_major (SiteConfig attribute) (SiteInfo attribute) p_major_ancestral (SiteInfo attribute) p_minor (SiteConfig attribute) (SiteInfo attribute) p_polarization (MaximumLikelihoodAncestralAnnotation property) parallelize (AdaptivePolarizationPrior attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Settings attribute) param_names (MaximumLikelihoodAncestralAnnotation attribute) params_mle (MaximumLikelihoodAncestralAnnotation attribute) params_mle_runs (MaximumLikelihoodAncestralAnnotation attribute) parse() (Parser method) parser (AncestralBaseStratification attribute) (BaseContextStratification attribute) (BaseTransitionStratification attribute) (ChunkedStratification attribute) Parser (class in sfsutils.parser) parser (ContigStratification attribute) (DegeneracyStratification attribute) (GenomePositionDependentStratification attribute) (RandomStratification attribute) (SnpEffStratification attribute) (SNPStratification attribute) (Stratification attribute) (SynonymyStratification attribute) (TransitionTransversionStratification attribute) (VEPStratification attribute) plot() (AbstractSpectrum method) (AdaptivePolarizationPrior method) (JointSFS method) (KingmanPolarizationPrior method) (PolarizationPrior method) (Spectra method) (Spectrum method) (TwoLocusSFS method) (TwoSFS method) plot_likelihoods() (MaximumLikelihoodAncestralAnnotation method) plot_surface() (JointSFS method) (TwoLocusSFS method) (TwoSFS method) plot_tree() (SiteInfo method) PolarizationPrior (class in sfsutils.annotation) polarize_probabilistically (Parser attribute) PolyAllelicFiltration (class in sfsutils.filtration) polymorphic (Spectra property) (Spectrum property) pool_branch_rates (JCSubstitutionModel attribute) (K2SubstitutionModel attribute) (SubstitutionModel attribute) pop_names (JointSFS attribute) (JointSpectra property) pops (Parser attribute) POS (Site attribute) (Variant attribute) prefix() (Spectra method) print() (Spectra method) prior (MaximumLikelihoodAncestralAnnotation attribute) probabilities (AdaptivePolarizationPrior attribute) (KingmanPolarizationPrior attribute) (PolarizationPrior attribute) R RandomStratification (class in sfsutils.parser) rate_params (SiteInfo attribute) REF (Site attribute) (Variant attribute) remove_overlaps() (Annotator static method) (Filterer static method) (GFFHandler static method) (Parser static method) rename() (Spectra method) reorder_levels() (Spectra method) replace_dots() (Spectra method) resample() (Spectra method) (Spectrum method) result (MaximumLikelihoodAncestralAnnotation attribute) retain_monomorphic (DeviantOutgroupFiltration attribute) rng (AdaptivePolarizationPrior attribute) (AdHocAncestralAnnotation attribute) (Annotator attribute) (Filterer attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) (RandomStratification attribute) (VCFHandler attribute) S samples (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) (MaximumParsimonyAncestralAnnotation attribute) (TskitVariantReader property) (VariantReader property) (ZarrVariantReader property) samples_mask (MaximumParsimonyAncestralAnnotation attribute) scale_theta() (Spectrum method) seed (AdaptivePolarizationPrior attribute) (AdHocAncestralAnnotation attribute) (Annotator attribute) (Filterer attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) (RandomStratification attribute) (VCFHandler attribute) select() (Spectra method) seqnames (TskitVariantReader property) (VariantReader property) (ZarrVariantReader property) sequence_length (TskitVariantReader property) (VariantReader property) (ZarrVariantReader property) set_mle_params() (MaximumLikelihoodAncestralAnnotation method) Settings (class in sfsutils.settings) sfs (Parser attribute) shape (AbstractSpectrum property) (JointSFS property) (JointSpectra property) (Spectrum property) (TwoLocusSFS property) (TwoSFS property) (TwoSpectra property) Site (class in sfsutils.io_handlers) SiteConfig (class in sfsutils.annotation) SiteInfo (class in sfsutils.annotation) sites (SiteConfig attribute) skip_non_polarized (Parser attribute) snpeff_mismatches (SynonymyAnnotation attribute) SnpEffStratification (class in sfsutils.parser) SNPFiltration (class in sfsutils.filtration) SNPStratification (class in sfsutils.parser) SNVFiltration (class in sfsutils.filtration) sort_types() (Spectra method) source (Annotator attribute) (Filterer attribute) (Parser attribute) Spectra (class in sfsutils.spectrum) Spectrum (class in sfsutils.spectrum) standard_kingman() (Spectrum static method) Stratification (class in sfsutils.parser) stratifications (Parser attribute) strict_mode (DeviantOutgroupFiltration attribute) subsample() (Spectra method) (Spectrum method) subsample_mode (AdHocAncestralAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) SubstitutionModel (class in sfsutils.annotation) symmetrize() (TwoLocusSFS method) (TwoSFS method) SynonymyAnnotation (class in sfsutils.annotation) SynonymyStratification (class in sfsutils.parser) T target_site_counter (Parser attribute) TargetSiteCounter (class in sfsutils.parser) Theta (Spectra property) theta (Spectra property) Theta (Spectrum property) theta (Spectrum property) to_dataframe() (Spectra method) to_dict() (AbstractSpectra method) (JointSpectra method) (Spectra method) (TwoSpectra method) to_est_sfs() (MaximumLikelihoodAncestralAnnotation method) to_file() (AbstractSpectra method) (AbstractSpectrum method) (JointSFS method) (JointSpectra method) (MaximumLikelihoodAncestralAnnotation method) (Spectra method) (Spectrum method) (TwoLocusSFS method) (TwoSFS method) (TwoSpectra method) to_json() (AbstractSpectrum method) (JointSFS method) (JointSpectra method) (MaximumLikelihoodAncestralAnnotation method) (Spectrum method) (TwoLocusSFS method) (TwoSFS method) (TwoSpectra method) to_list() (Spectra method) (Spectrum method) to_numpy() (Spectra method) (Spectrum method) to_spectra() (Spectra method) (Spectrum method) to_spectrum() (Spectra method) TransitionTransversionStratification (class in sfsutils.parser) tree_sequence (TskitVariantReader property) TskitVariantReader (class in sfsutils.io_handlers) TskitVariantWriter (class in sfsutils.io_handlers) two_sfs (Parser attribute) two_sfs_offset (Parser attribute) TwoLocusSFS (class in sfsutils.spectrum) TwoSFS (class in sfsutils.spectrum) TwoSpectra (class in sfsutils.spectrum) types (AbstractSpectra property) (JointSpectra property) (Spectra property) (TwoSpectra property) U unzip_if_zipped() (Annotator static method) (BaseContextStratification static method) (FASTAHandler static method) (FileHandler static method) (Filterer static method) (GFFHandler static method) (Parser static method) (VCFHandler static method) use_parser (MaskedFiltration attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) V validate_bounds() (JCSubstitutionModel static method) (K2SubstitutionModel static method) (SubstitutionModel static method) Variant (class in sfsutils.io_handlers) VariantReader (class in sfsutils.io_handlers) VariantWriter (class in sfsutils.io_handlers) vcf (Annotator attribute) (Filterer attribute) (Parser attribute) (VCFHandler attribute) VCFHandler (class in sfsutils.io_handlers) VCFVariantWriter (class in sfsutils.io_handlers) vep_mismatches (SynonymyAnnotation attribute) VEPStratification (class in sfsutils.parser) W w (TwoLocusSFS attribute) (TwoSFS attribute) with_traceback() (NoTypeException method) write() (TskitVariantWriter method) (VariantWriter method) (VCFVariantWriter method) (ZarrVariantWriter method) Z ZarrVariantReader (class in sfsutils.io_handlers) ZarrVariantWriter (class in sfsutils.io_handlers)
