Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | X _ __init__() (AdaptivePolarizationPrior method) (AdHocAncestralAnnotation method) (AllFiltration method) (AncestralAlleleAnnotation method) (AncestralBaseStratification method) (Annotation method) (Annotator method) (BaseContextStratification method) (BaseInference method) (BaseTransitionStratification method) (BiasedGCConversionFiltration method) (ChunkedStratification method) (CodingSequenceFiltration method) (Config method) (ContigFiltration method) (ContigStratification method) (Covariate method) (DegeneracyAnnotation method) (DegeneracyStratification method) (DeviantOutgroupFiltration method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (ExistingOutgroupFiltration method) (Filterer method) (Filtration method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (GenomePositionDependentStratification method) (InferenceResult method) (JCSubstitutionModel method) (JointInference method) (K2SubstitutionModel method) (KingmanPolarizationPrior method) (MaskedFiltration method) (MaximumLikelihoodAncestralAnnotation method) (MaximumParsimonyAncestralAnnotation method) (NoFiltration method) (Parametrization method) (Parser method) (PolarizationPrior method) (PolyAllelicFiltration method) (RandomStratification method) (SharedParams method) (Simulation 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) (VEPStratification method) A AdaptivePolarizationPrior (class in fastdfe.annotation) AdHocAncestralAnnotation (class in fastdfe.annotation) adjust_target_sites (MaximumLikelihoodAncestralAnnotation attribute) aliases (Annotator attribute) (BaseContextStratification attribute) (Filterer attribute) (Parser attribute) all (Spectra property) AllFiltration (class in fastdfe.filtration) allow_divergence (AdaptivePolarizationPrior attribute) (KingmanPolarizationPrior attribute) (PolarizationPrior attribute) alpha (BaseInference property) (JointInference property) AncestralAlleleAnnotation (class in fastdfe.annotation) AncestralBaseStratification (class in fastdfe.parser) annotate() (Annotator method) annotate_site() (AdHocAncestralAnnotation method) (AncestralAlleleAnnotation method) (Annotation method) (DegeneracyAnnotation method) (MaximumLikelihoodAncestralAnnotation method) (MaximumParsimonyAncestralAnnotation method) (SynonymyAnnotation method) Annotation (class in fastdfe.annotation) annotations (Annotator attribute) (Parser attribute) Annotator (class in fastdfe.annotation) apply() (Covariate method) apply_default() (Covariate method) B BaseContextStratification (class in fastdfe.parser) BaseInference (class in fastdfe.base_inference) BaseTransitionStratification (class in fastdfe.parser) BaseType (class in fastdfe.annotation) BiasedGCConversionFiltration (class in fastdfe.filtration) bootstrap() (BaseInference method) (JointInference method) bootstrap_if_required() (JointInference method) bootstrap_results (BaseInference attribute) (JointInference attribute) bootstraps (BaseInference attribute) (DFE attribute) (InferenceResult attribute) (JointInference attribute) bounds (BaseInference attribute) (Covariate attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JCSubstitutionModel attribute) (JointInference attribute) (K2SubstitutionModel attribute) (Parametrization attribute) (SubstitutionModel attribute) bounds_scale (Covariate attribute) C cache (Annotator attribute) (BaseContextStratification attribute) (Filterer attribute) (Parser attribute) cache() (JCSubstitutionModel method) (K2SubstitutionModel method) (SubstitutionModel method) callback (Covariate attribute) cd (CodingSequenceFiltration attribute) cdf() (DFE method) check_fixed_params_exist() (BaseInference method) (JointInference method) check_no_shared_params_fixed() (JointInference method) check_shared_params() (JointInference method) chunk_sizes (ChunkedStratification attribute) ChunkedStratification (class in fastdfe.parser) CodingSequenceFiltration (class in fastdfe.filtration) combine() (Spectra method) compare_nested() (BaseInference method) (JointInference method) compare_nested_models() (BaseInference method) (JointInference method) compute_histogram() (Inference static method) confidence_threshold (MaximumLikelihoodAncestralAnnotation attribute) Config (class in fastdfe.config) config (InferenceResult attribute) configs (MaximumLikelihoodAncestralAnnotation attribute) contig (BaseContextStratification attribute) ContigFiltration (class in fastdfe.filtration) contigs (ContigFiltration attribute) (ContigStratification attribute) ContigStratification (class in fastdfe.parser) copy() (Spectra method) (Spectrum method) count() (TargetSiteCounter method) count_sites() (Annotator method) (Filterer method) (Parser 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) Covariate (class in fastdfe.optimization) covariates (JointInference attribute) create_config() (BaseInference method) (JointInference method) create_polydfe_init_file() (Config method) create_polydfe_sfs_config() (Config method) D DegeneracyAnnotation (class in fastdfe.annotation) DegeneracyStratification (class in fastdfe.parser) DeviantOutgroupFiltration (class in fastdfe.filtration) DFE (class in fastdfe.parametrization) dfe (InferenceResult attribute) (Simulation attribute) DiscreteFractionalParametrization (class in fastdfe.parametrization) DiscreteParametrization (class in fastdfe.parametrization) discretization (BaseInference attribute) (JointInference attribute) (Simulation attribute) discretize() (DFE method) DisplacedGammaParametrization (class in fastdfe.parametrization) do_bootstrap (BaseInference attribute) (JointInference attribute) download_file() (Annotator class method) (BaseContextStratification class method) (Filterer class method) (Parser class method) download_if_url() (Annotator method) (BaseContextStratification method) (Filterer method) (Parser method) drop_empty() (Spectra method) drop_sparse() (Spectra method) drop_zero_entries() (Spectra method) E errors (DegeneracyAnnotation attribute) (SynonymyAnnotation attribute) evaluate_likelihood() (BaseInference method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) exclude (AdHocAncestralAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) exclude_samples (MaskedFiltration attribute) (Parser attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) execution_time (BaseInference attribute) (JointInference attribute) ExistingOutgroupFiltration (class in fastdfe.filtration) F fasta (Annotator attribute) (BaseContextStratification attribute) (Filterer attribute) (Parser attribute) fastdfe.annotation module fastdfe.filtration module fastdfe.parametrization module fastdfe.parser module filter() (Filterer method) filter_site() (AllFiltration method) (BiasedGCConversionFiltration method) (CodingSequenceFiltration method) (ContigFiltration method) (DeviantOutgroupFiltration method) (ExistingOutgroupFiltration method) (Filtration method) (MaskedFiltration method) (NoFiltration method) (PolyAllelicFiltration method) (SNPFiltration method) (SNVFiltration method) Filterer (class in fastdfe.filtration) Filtration (class in fastdfe.filtration) filtrations (Filterer attribute) (Parser attribute) first_node_ancestral (SiteInfo attribute) fix_transition_transversion_ratio (K2SubstitutionModel attribute) fixed_params (BaseInference attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (JCSubstitutionModel attribute) (JointInference attribute) (K2SubstitutionModel attribute) (SubstitutionModel attribute) fold() (Spectra method) (Spectrum method) folded (BaseInference attribute) (JointInference attribute) freeze() (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (Parametrization method) from_config() (BaseInference class method) (JointInference class method) from_config_file() (BaseInference class method) (JointInference class method) from_data() (MaximumLikelihoodAncestralAnnotation class method) from_dataframe() (MaximumLikelihoodAncestralAnnotation class method) (Spectra static method) from_dict() (Config static method) (Spectra static method) from_est_sfs() (MaximumLikelihoodAncestralAnnotation class method) from_file() (BaseInference class method) (Config class method) (DFE class method) (DiscreteFractionalParametrization class method) (DiscreteParametrization class method) (DisplacedGammaParametrization class method) (GammaDiscreteParametrization class method) (GammaExpParametrization class method) (InferenceResult class method) (JointInference class method) (MaximumLikelihoodAncestralAnnotation class method) (Parametrization class method) (Spectra class method) (Spectrum static method) from_json() (BaseInference class method) (Config static method) (DFE class method) (DiscreteFractionalParametrization class method) (DiscreteParametrization class method) (DisplacedGammaParametrization class method) (GammaDiscreteParametrization class method) (GammaExpParametrization class method) (InferenceResult class method) (JointInference class method) (MaximumLikelihoodAncestralAnnotation class method) (Parametrization 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) from_yaml() (Config static method) G GammaDiscreteParametrization (class in fastdfe.parametrization) GammaExpParametrization (class in fastdfe.parametrization) GenomePositionDependentStratification (class in fastdfe.parser) get_aliases() (Annotator method) (BaseContextStratification method) (Filterer method) (Parser method) get_alpha() (BaseInference method) (JointInference method) (Simulation method) get_base_index() (AdHocAncestralAnnotation class method) (MaximumLikelihoodAncestralAnnotation class method) get_base_string() (AdHocAncestralAnnotation static method) (MaximumLikelihoodAncestralAnnotation static method) get_bootstrap_dfes() (DFE method) get_bootstrap_param_names() (BaseInference method) (JointInference method) get_bootstrap_params() (BaseInference method) (JointInference method) get_bound() (JCSubstitutionModel method) (K2SubstitutionModel method) get_bounds() (JCSubstitutionModel method) (K2SubstitutionModel method) (SubstitutionModel method) get_bounds_linear() (BaseInference method) (JointInference method) get_cdf() (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization static method) (GammaDiscreteParametrization static method) (GammaExpParametrization static method) (Parametrization method) get_contig() (Annotator method) (BaseContextStratification method) (Filterer method) (Parser method) get_contig_names() (Annotator method) (BaseContextStratification method) (Filterer method) (Parser method) get_counts() (BaseInference method) (JointInference method) get_degeneracy (DegeneracyStratification attribute) get_dfe() (BaseInference method) (JointInference method) get_discretized() (BaseInference method) (Inference static method) (JointInference method) get_empty() (Spectra method) get_errors_params_mle() (Inference static method) get_filename() (Annotator static method) (BaseContextStratification static method) (Filterer static method) (Parser static method) get_fixed_param_names() (BaseInference method) (JointInference method) get_folded_spectra() (MaximumLikelihoodAncestralAnnotation method) get_inferences() (JointInference method) get_inferred_site_info() (MaximumLikelihoodAncestralAnnotation method) get_n_optimized() (BaseInference method) (JointInference method) get_neutral() (Spectrum static method) get_neutral_sfs() (Simulation static method) get_observed_transition_transversion_ratio() (MaximumLikelihoodAncestralAnnotation method) get_optimized_param_names() (BaseInference method) (JointInference 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) get_pdf() (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization static method) (GammaDiscreteParametrization static method) (GammaExpParametrization static method) (Parametrization method) get_polydfe_model() (Config method) get_residual() (BaseInference method) (JointInference method) get_scales_linear() (BaseInference method) (JointInference method) get_shared_param_names() (JointInference method) get_site_info() (MaximumLikelihoodAncestralAnnotation method) get_spectra() (BaseInference method) (JointInference method) (Simulation method) get_stats_discretized() (BaseInference method) (Inference static method) (JointInference method) get_summary() (BaseInference method) (JointInference 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_wright_fisher() (Simulation method) get_x0() (BaseInference method) (JCSubstitutionModel static method) (JointInference method) (K2SubstitutionModel static method) (SubstitutionModel static method) gff (Annotator attribute) (Filterer attribute) (Parser attribute) H has_div (Spectra property) (Spectrum property) has_dots() (Spectra method) hash() (Annotator static method) (BaseContextStratification static method) (Filterer static method) (Parser static method) I include_samples (MaskedFiltration attribute) (Parser attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) infer() (MaximumLikelihoodAncestralAnnotation method) Inference (class in fastdfe.abstract_inference) InferenceResult (class in fastdfe.base_inference) info_ancestral (Annotator attribute) (Filterer attribute) (Parser attribute) info_ancestral_prob (Parser attribute) info_tag (SnpEffStratification attribute) (VEPStratification attribute) ingroup_mask (DeviantOutgroupFiltration attribute) ingroups (AdHocAncestralAnnotation attribute) (DeviantOutgroupFiltration attribute) (MaximumLikelihoodAncestralAnnotation attribute) interval_sizes (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) intervals (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) is_filtered() (Filterer method) is_folded() (Spectra method) (Spectrum method) is_monotonic() (MaximumLikelihoodAncestralAnnotation method) is_synonymous() (SynonymyAnnotation static method) is_url() (Annotator static method) (BaseContextStratification static method) (Filterer static method) (Parser static method) J JCSubstitutionModel (class in fastdfe.annotation) joint_inference_makes_sense() (JointInference method) joint_inferences (JointInference attribute) JointInference (class in fastdfe.joint_inference) K k (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (Spectra property) K2SubstitutionModel (class in fastdfe.annotation) KingmanPolarizationPrior (class in fastdfe.annotation) L L2_residual (BaseInference attribute) (JointInference attribute) likelihood (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) likelihoods (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) load_fasta() (Annotator method) (BaseContextStratification method) (Filterer method) (Parser method) load_vcf() (Annotator method) (Filterer method) (Parser method) locked (BaseInference attribute) (JointInference attribute) lrt() (BaseInference method) (JointInference method) M MAJOR (BaseType attribute) major_ancestral (SiteInfo attribute) major_base (SiteConfig attribute) (SiteInfo attribute) marginal_inferences (JointInference attribute) marginals_without_all() (JointInference method) MaskedFiltration (class in fastdfe.filtration) max_sites (Annotator attribute) (Filterer attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) MaximumLikelihoodAncestralAnnotation (class in fastdfe.annotation) MaximumParsimonyAncestralAnnotation (class in fastdfe.annotation) merge_groups() (Spectra method) MINOR (BaseType attribute) minor_base (SiteConfig attribute) (SiteInfo attribute) misidentify() (Spectrum method) mismatches (DegeneracyAnnotation attribute) (SynonymyAnnotation attribute) model (BaseInference attribute) (DFE attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Simulation attribute) module fastdfe.annotation fastdfe.filtration fastdfe.parametrization fastdfe.parser multiplicity (SiteConfig attribute) mutate() (SynonymyAnnotation static method) N n (BaseInference attribute) (JointInference attribute) (Parser attribute) (Simulation attribute) (Spectra property) (Spectrum property) n_annotated (AdHocAncestralAnnotation attribute) (AncestralAlleleAnnotation attribute) (Annotation attribute) (DegeneracyAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) (MaximumParsimonyAncestralAnnotation attribute) (SynonymyAnnotation attribute) n_bootstrap_retries (BaseInference attribute) (JointInference attribute) n_bootstraps (BaseInference attribute) (JointInference attribute) n_chunks (ChunkedStratification attribute) n_div (Spectra property) (Spectrum property) n_filtered (AllFiltration attribute) (BiasedGCConversionFiltration attribute) (CodingSequenceFiltration attribute) (ContigFiltration 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_processed (CodingSequenceFiltration attribute) n_runs (AdaptivePolarizationPrior attribute) (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) n_samples (TargetSiteCounter attribute) n_samples_target_sites (MaximumLikelihoodAncestralAnnotation attribute) n_sites (Annotator property) (Filterer property) (MaximumLikelihoodAncestralAnnotation attribute) (Parser property) (Simulation attribute) (Spectra property) (Spectrum 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 fastdfe.filtration) normalize() (Spectra method) (Spectrum method) num_bins (RandomStratification attribute) O optimization (BaseInference attribute) (JointInference attribute) 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) (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) param (Covariate attribute) param_names (BaseInference property) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference property) (MaximumLikelihoodAncestralAnnotation attribute) (Parametrization attribute) Parametrization (class in fastdfe.parametrization) params (DFE attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (SharedParams attribute) (Simulation attribute) params_mle (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) params_mle_raw (JointInference attribute) params_mle_runs (MaximumLikelihoodAncestralAnnotation attribute) parse() (Parser method) parse_polydfe_init_file() (Config method) parse_polydfe_sfs_config() (Config method) parser (AncestralBaseStratification attribute) (BaseContextStratification attribute) (BaseTransitionStratification attribute) (ChunkedStratification attribute) Parser (class in fastdfe.parser) parser (ContigStratification attribute) (DegeneracyStratification attribute) (GenomePositionDependentStratification attribute) (RandomStratification attribute) (SnpEffStratification attribute) (SNPStratification attribute) (Stratification attribute) (SynonymyStratification attribute) (TransitionTransversionStratification attribute) (VEPStratification attribute) pdf() (DFE method) perform_lrt_covariates() (JointInference method) perform_lrt_shared() (JointInference method) plot() (AdaptivePolarizationPrior method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (KingmanPolarizationPrior method) (Parametrization method) (PolarizationPrior method) (Spectra method) (Spectrum method) plot_all() (BaseInference method) (JointInference method) plot_bucket_sizes() (BaseInference method) (JointInference method) plot_continuous() (BaseInference method) (Inference static method) (JointInference method) plot_covariate() (JointInference method) plot_discretized() (BaseInference method) (Inference static method) (JointInference method) plot_inferred_parameters() (BaseInference method) (Inference static method) (JointInference method) plot_inferred_parameters_boxplot() (BaseInference method) (Inference static method) (JointInference method) plot_interval_density() (BaseInference method) (JointInference method) plot_likelihoods() (BaseInference method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) plot_many() (DFE static method) plot_nested_models() (BaseInference method) (JointInference method) plot_observed_sfs() (BaseInference method) (JointInference method) plot_sfs_comparison() (BaseInference method) (JointInference method) plot_tree() (SiteInfo method) PolarizationPrior (class in fastdfe.annotation) polarize_probabilistically (Parser attribute) PolyAllelicFiltration (class in fastdfe.filtration) polymorphic (Spectra property) (Spectrum property) pool_branch_rates (JCSubstitutionModel attribute) (K2SubstitutionModel attribute) (SubstitutionModel attribute) prefix() (Spectra method) print() (Spectra method) prior (MaximumLikelihoodAncestralAnnotation attribute) probabilities (AdaptivePolarizationPrior attribute) (KingmanPolarizationPrior attribute) (PolarizationPrior attribute) R raise_if_locked() (BaseInference method) (JointInference method) RandomStratification (class in fastdfe.parser) rate_params (SiteInfo attribute) remove_overlaps() (Annotator static method) (Filterer static method) (Parser static method) rename() (Spectra method) reorder_levels() (Spectra method) replace_dots() (Spectra method) resample() (Spectra method) (Spectrum method) result (BaseInference attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) retain_monomorphic (DeviantOutgroupFiltration attribute) rng (AdaptivePolarizationPrior attribute) (AdHocAncestralAnnotation attribute) (Annotator attribute) (BaseInference attribute) (Filterer attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) (RandomStratification attribute) run() (BaseInference method) (JointInference method) (Simulation method) run_if_required() (BaseInference method) (JointInference method) run_joint_without_covariates() (JointInference method) runs (BaseInference attribute) (InferenceResult attribute) (JointInference attribute) S samples (DeviantOutgroupFiltration attribute) (ExistingOutgroupFiltration attribute) (MaximumParsimonyAncestralAnnotation attribute) scale_theta() (Spectrum method) scales (BaseInference attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute) seed (AdaptivePolarizationPrior attribute) (AdHocAncestralAnnotation attribute) (Annotator attribute) (BaseInference attribute) (Filterer attribute) (JointInference attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) (RandomStratification attribute) select() (Spectra method) set_mle_params() (MaximumLikelihoodAncestralAnnotation method) sfs (Parser attribute) sfs_mle (BaseInference attribute) (JointInference attribute) sfs_neut (BaseInference attribute) (JointInference attribute) (Simulation attribute) sfs_sel (BaseInference attribute) (JointInference attribute) (Simulation attribute) shared_params (JointInference attribute) SharedParams (class in fastdfe.optimization) Simulation (class in fastdfe.simulation) SiteConfig (class in fastdfe.annotation) SiteInfo (class in fastdfe.annotation) sites (SiteConfig attribute) skip_non_polarized (Parser attribute) snpeff_mismatches (SynonymyAnnotation attribute) SnpEffStratification (class in fastdfe.parser) SNPFiltration (class in fastdfe.filtration) SNPStratification (class in fastdfe.parser) SNVFiltration (class in fastdfe.filtration) sort_types() (Spectra method) Spectra (class in fastdfe.spectrum) spectra (InferenceResult attribute) Spectrum (class in fastdfe.spectrum) standard_kingman() (Spectrum static method) Stratification (class in fastdfe.parser) stratifications (Parser attribute) strict_mode (DeviantOutgroupFiltration attribute) submodels (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (Parametrization attribute) subsample() (Spectra method) (Spectrum method) subsample_mode (AdHocAncestralAnnotation attribute) (MaximumLikelihoodAncestralAnnotation attribute) (Parser attribute) SubstitutionModel (class in fastdfe.annotation) SynonymyAnnotation (class in fastdfe.annotation) SynonymyStratification (class in fastdfe.parser) T target_site_counter (Parser attribute) TargetSiteCounter (class in fastdfe.parser) theta (BaseInference attribute) (JointInference attribute) (Simulation attribute) Theta (Spectra property) theta (Spectra property) Theta (Spectrum property) theta (Spectrum property) to_dataframe() (Spectra method) to_dict() (Config method) (Spectra method) to_est_sfs() (MaximumLikelihoodAncestralAnnotation method) to_file() (BaseInference method) (Config method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (InferenceResult method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) (Parametrization method) (Spectra method) (Spectrum method) to_fractional() (DiscreteFractionalParametrization method) to_json() (BaseInference method) (Config method) (DFE method) (DiscreteFractionalParametrization method) (DiscreteParametrization method) (DisplacedGammaParametrization method) (GammaDiscreteParametrization method) (GammaExpParametrization method) (InferenceResult method) (JointInference method) (MaximumLikelihoodAncestralAnnotation method) (Parametrization method) to_list() (Spectra method) (Spectrum method) to_nominal() (DiscreteFractionalParametrization method) to_numpy() (Spectra method) (Spectrum method) to_spectra() (Spectra method) (Spectrum method) to_spectrum() (Spectra method) to_yaml() (Config method) TransitionTransversionStratification (class in fastdfe.parser) types (JointInference attribute) (SharedParams attribute) (Spectra property) U unzip_if_zipped() (Annotator static method) (BaseContextStratification static method) (Filterer static method) (Parser static method) update() (Config method) use_parser (MaskedFiltration attribute) (PolyAllelicFiltration attribute) (SNPFiltration attribute) V validate_bounds() (JCSubstitutionModel static method) (K2SubstitutionModel static method) (SubstitutionModel static method) values (Covariate attribute) vcf (Annotator attribute) (Filterer attribute) (Parser attribute) vep_mismatches (SynonymyAnnotation attribute) VEPStratification (class in fastdfe.parser) X x0 (BaseInference attribute) (Covariate attribute) (DiscreteFractionalParametrization attribute) (DiscreteParametrization attribute) (DisplacedGammaParametrization attribute) (GammaDiscreteParametrization attribute) (GammaExpParametrization attribute) (JointInference attribute) (Parametrization attribute)
