Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W _ __bool__() (skbio.alignment.TabularMSA method) (skbio.sequence.Sequence method) __call__() (skbio.alignment.StripedSmithWaterman method) (skbio.workflow.method method) (skbio.workflow.requires method) (skbio.workflow.Workflow method) __contains__() (skbio.alignment.TabularMSA method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) __copy__() (skbio.alignment.TabularMSA method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.IntervalMetadataMixin method) (skbio.metadata.MetadataMixin method) (skbio.metadata.PositionalMetadataMixin method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) __deepcopy__() (skbio.alignment.TabularMSA method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.IntervalMetadataMixin method) (skbio.metadata.MetadataMixin method) (skbio.metadata.PositionalMetadataMixin method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) __eq__() (skbio.alignment.TabularMSA method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.IntervalMetadataMixin method) (skbio.metadata.MetadataColumn method) (skbio.metadata.MetadataMixin method) (skbio.metadata.PositionalMetadataMixin method) (skbio.metadata.SampleMetadata method) (skbio.sequence.GeneticCode method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) __get__() (skbio.util.classproperty method) __getitem__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.TabularMSA method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) (skbio.tree.TreeNode method) __iter__() (skbio.alignment.TabularMSA method) (skbio.sequence.Sequence method) (skbio.table.Table method) (skbio.tree.TreeNode method) __len__() (skbio.alignment.TabularMSA method) (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) __ne__() (skbio.alignment.TabularMSA method) (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) (skbio.metadata.IntervalMetadataMixin method) (skbio.metadata.MetadataColumn method) (skbio.metadata.MetadataMixin method) (skbio.metadata.PositionalMetadataMixin method) (skbio.metadata.SampleMetadata method) (skbio.sequence.GeneticCode method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) __reversed__() (skbio.alignment.TabularMSA method) (skbio.sequence.Sequence method) __set__() (skbio.util.classproperty method) __setstate__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.StripedSmithWaterman method) __str__() (skbio.alignment.AlignmentStructure method) (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.embedding.EmbeddingVector method) (skbio.embedding.SequenceEmbedding method) (skbio.sequence.GeneticCode method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) A accumulate_to_ancestor() (skbio.tree.TreeNode method) ace() (in module skbio.diversity.alpha) add() (skbio.metadata.IntervalMetadata method) add_format() (skbio.io.registry.IORegistry method) add_group_metadata() (skbio.table.Table method) add_metadata() (skbio.table.Table method) align_to() (skbio.table.Table method) align_to_dataframe() (skbio.table.Table method) align_tree() (skbio.table.Table method) aligned_query_sequence (skbio.alignment.AlignmentStructure attribute) aligned_target_sequence (skbio.alignment.AlignmentStructure attribute) AlignmentStructure (class in skbio.alignment) AlignPath (class in skbio.alignment) alpha_diversity() (in module skbio.diversity) alphabet (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) (skbio.sequence.SubstitutionMatrix attribute) alr() (in module skbio.stats.composition) alr_inv() (in module skbio.stats.composition) ancestors() (skbio.tree.TreeNode method) ancom() (in module skbio.stats.composition) anosim() (in module skbio.stats.distance) append() (skbio.alignment.TabularMSA method) (skbio.tree.TreeNode method) ascii_art() (skbio.tree.TreeNode method) assert_data_frame_almost_equal() (in module skbio.util) assert_ordination_results_equal() (in module skbio.util) assign_ids() (skbio.tree.TreeNode method) assign_supports() (skbio.tree.TreeNode method) AverageGradientANOVA (class in skbio.stats.gradient) B berger_parker_d() (in module skbio.diversity.alpha) beta_diversity() (in module skbio.diversity) between() (skbio.stats.distance.DissimilarityMatrix method) bifurcate() (skbio.tree.TreeNode method) bioenv() (in module skbio.stats.distance) bipart() (skbio.tree.TreeNode method) biparts() (skbio.tree.TreeNode method) block_beta_diversity() (in module skbio.diversity) bme() (in module skbio.tree) bounds (skbio.metadata.Interval attribute) brillouin_d() (in module skbio.diversity.alpha) by_name() (skbio.sequence.SubstitutionMatrix class method) bytes() (skbio.embedding.Embedding method) C ca() (in module skbio.stats.ordination) cache_attr() (skbio.tree.TreeNode method) cardinal_to_ordinal() (in module skbio.util) CategoricalMetadataColumn (class in skbio.metadata) CategoryResults (class in skbio.stats.gradient) cca() (in module skbio.stats.ordination) centralize() (in module skbio.stats.composition) chao1() (in module skbio.diversity.alpha) chao1_ci() (in module skbio.diversity.alpha) cigar (skbio.alignment.AlignmentStructure attribute) classproperty (class in skbio.util) clear_caches() (skbio.tree.TreeNode method) closure() (in module skbio.stats.composition) clr() (in module skbio.stats.composition) clr_inv() (in module skbio.stats.composition) collapse() (skbio.table.Table method) column_count (skbio.metadata.SampleMetadata attribute) columns (skbio.metadata.SampleMetadata attribute) compare_biparts() (skbio.tree.TreeNode method) compare_cophenet() (skbio.tree.TreeNode method) compare_rfd() (skbio.tree.TreeNode method) compare_subsets() (skbio.tree.TreeNode method) compare_tip_distances() (skbio.tree.TreeNode method) compare_wrfd() (skbio.tree.TreeNode method) complement() (skbio.sequence.NucleotideMixin method) complement_map (skbio.sequence.DNA attribute) (skbio.sequence.NucleotideMixin attribute) (skbio.sequence.RNA attribute) concat() (skbio.metadata.IntervalMetadata class method) (skbio.sequence.Sequence class method) (skbio.table.Table method) condensed_form() (skbio.stats.distance.DistanceMatrix method) confidence_bound() (in module skbio.stats.power) consensus() (skbio.alignment.TabularMSA method) conservation() (skbio.alignment.TabularMSA method) cophenet() (skbio.tree.TreeNode method) copy() (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) (skbio.tree.TreeNode method) corr() (in module skbio.stats.ordination) count() (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) create_caches() (skbio.tree.TreeNode method) create_format() (in module skbio.io.registry) (skbio.io.registry.IORegistry method) D data (skbio.stats.distance.DissimilarityMatrix attribute) data() (skbio.table.Table method) deepcopy() (skbio.tree.TreeNode method) default_gap_char (skbio.sequence.DNA attribute) (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) (skbio.sequence.RNA attribute) default_write_format (skbio.alignment.TabularMSA attribute) (skbio.embedding.ProteinEmbedding attribute) (skbio.embedding.ProteinVector attribute) (skbio.metadata.IntervalMetadata attribute) (skbio.metadata.SampleMetadata attribute) (skbio.sequence.Sequence attribute) (skbio.stats.distance.DissimilarityMatrix attribute) (skbio.stats.ordination.OrdinationResults attribute) (skbio.table.Table attribute) (skbio.tree.TreeNode attribute) definite_chars (skbio.sequence.DNA attribute) (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) (skbio.sequence.RNA attribute) definites() (skbio.sequence.GrammaredSequence method) degap() (skbio.sequence.GrammaredSequence method) degenerate_chars (skbio.sequence.GrammaredSequence attribute) degenerate_map (skbio.sequence.DNA attribute) (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) (skbio.sequence.RNA attribute) degenerates() (skbio.sequence.GrammaredSequence method) del_metadata() (skbio.table.Table method) delimited_self() (skbio.table.Table method) depth() (skbio.tree.TreeNode method) descending_branch_length() (skbio.tree.TreeNode method) descriptive_equality() (skbio.table.Table method) dirmult_lme() (in module skbio.stats.composition) dirmult_ttest() (in module skbio.stats.composition) DissimilarityMatrix (class in skbio.stats.distance) distance() (skbio.sequence.Sequence method) (skbio.tree.TreeNode method) DistanceMatrix (class in skbio.stats.distance) DNA (class in skbio.sequence) dominance() (in module skbio.diversity.alpha) doubles() (in module skbio.diversity.alpha) drop() (skbio.metadata.Interval method) (skbio.metadata.IntervalMetadata method) drop_missing_values() (skbio.metadata.MetadataColumn method) dropped (skbio.metadata.Interval attribute) dtype (skbio.alignment.TabularMSA attribute) (skbio.stats.distance.DissimilarityMatrix attribute) (skbio.table.Table attribute) E e_matrix() (in module skbio.stats.ordination) EfficiencyWarning embed_vec_to_dataframe() (in module skbio.embedding) embed_vec_to_distances() (in module skbio.embedding) embed_vec_to_numpy() (in module skbio.embedding) embed_vec_to_ordination() (in module skbio.embedding) Embedding (class in skbio.embedding) embedding (skbio.embedding.Embedding attribute) (skbio.embedding.EmbeddingVector attribute) EmbeddingVector (class in skbio.embedding) enspie() (in module skbio.diversity.alpha) esty_ci() (in module skbio.diversity.alpha) example_table (in module skbio.table) exists() (skbio.table.Table method) expand_degenerates() (skbio.sequence.GrammaredSequence method) extend() (skbio.alignment.TabularMSA method) (skbio.tree.TreeNode method) F f_matrix() (in module skbio.stats.ordination) faith_pd() (in module skbio.diversity.alpha) filter() (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) filter_columns() (skbio.metadata.SampleMetadata method) filter_ids() (skbio.metadata.MetadataColumn method) (skbio.metadata.SampleMetadata method) find() (skbio.tree.TreeNode method) find_all() (skbio.tree.TreeNode method) find_by_func() (skbio.tree.TreeNode method) find_by_id() (skbio.tree.TreeNode method) find_duplicates() (in module skbio.util) find_motifs() (skbio.sequence.DNA method) (skbio.sequence.GrammaredSequence method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) find_with_regex() (skbio.sequence.Sequence method) FirstDifferenceGradientANOVA (class in skbio.stats.gradient) fisher_alpha() (in module skbio.diversity.alpha) Format (class in skbio.io.registry) frequencies() (skbio.sequence.Sequence method) from_adjacency() (skbio.table.Table static method) from_bits() (skbio.alignment.AlignPath class method) (skbio.alignment.PairAlignPath class method) from_cigar() (skbio.alignment.PairAlignPath class method) from_coordinates() (skbio.alignment.AlignPath class method) from_dict() (skbio.alignment.TabularMSA class method) (skbio.sequence.SubstitutionMatrix class method) from_hdf5() (skbio.table.Table class method) from_indices() (skbio.alignment.AlignPath class method) from_iterable() (skbio.stats.distance.DissimilarityMatrix class method) (skbio.stats.distance.DistanceMatrix class method) from_json() (skbio.table.Table class method) from_linkage_matrix() (skbio.tree.TreeNode class method) from_ncbi() (skbio.sequence.GeneticCode class method) from_path_seqs() (skbio.alignment.TabularMSA class method) from_tabular() (skbio.alignment.AlignPath class method) from_taxdump() (skbio.tree.TreeNode class method) from_taxonomy() (skbio.tree.TreeNode class method) from_tsv() (skbio.table.Table static method) fuzzy (skbio.metadata.Interval attribute) G gap_chars (skbio.sequence.DNA attribute) (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) (skbio.sequence.RNA attribute) gap_frequencies() (skbio.alignment.TabularMSA method) gaps() (skbio.sequence.GrammaredSequence method) gc_content() (skbio.sequence.NucleotideMixin method) gc_frequency() (skbio.sequence.NucleotideMixin method) GeneticCode (class in skbio.sequence) get_alpha_diversity_metrics() (in module skbio.diversity) get_beta_diversity_metrics() (in module skbio.diversity) get_column() (skbio.metadata.SampleMetadata method) get_data_path() (in module skbio.util) get_ids() (skbio.metadata.MetadataColumn method) (skbio.metadata.SampleMetadata method) get_max_distance() (skbio.tree.TreeNode method) get_missing() (skbio.metadata.MetadataColumn method) get_names() (skbio.sequence.SubstitutionMatrix class method) get_reader() (skbio.io.registry.IORegistry method) get_rng() (in module skbio.util) get_sniffer() (skbio.io.registry.IORegistry method) get_table_density() (skbio.table.Table method) get_trajectories() (skbio.stats.gradient.GradientANOVA method) get_value() (skbio.metadata.MetadataColumn method) get_value_by_ids() (skbio.table.Table method) get_writer() (skbio.io.registry.IORegistry method) gini_index() (in module skbio.diversity.alpha) global_pairwise_align() (in module skbio.alignment) global_pairwise_align_nucleotide() (in module skbio.alignment) global_pairwise_align_protein() (in module skbio.alignment) gme() (in module skbio.tree) goods_coverage() (in module skbio.diversity.alpha) GradientANOVA (class in skbio.stats.gradient) GradientANOVAResults (class in skbio.stats.gradient) GrammaredSequence (class in skbio.sequence) group_metadata() (skbio.table.Table method) GroupResults (class in skbio.stats.gradient) H hamming() (in module skbio.sequence.distance) has_caches() (skbio.tree.TreeNode method) has_children() (skbio.tree.TreeNode method) has_definites() (skbio.sequence.GrammaredSequence method) has_degenerates() (skbio.sequence.GrammaredSequence method) has_gaps() (skbio.sequence.GrammaredSequence method) has_interval_metadata() (skbio.metadata.IntervalMetadataMixin method) has_metadata() (skbio.metadata.MetadataMixin method) has_missing_values() (skbio.metadata.MetadataColumn method) has_nondegenerates() (skbio.sequence.GrammaredSequence method) has_positional_metadata() (skbio.metadata.PositionalMetadataMixin method) has_stops() (skbio.sequence.Protein method) head() (skbio.table.Table method) height() (skbio.tree.TreeNode method) heip_e() (in module skbio.diversity.alpha) highest_priority (skbio.workflow.method attribute) hill() (in module skbio.diversity.alpha) hommola_cospeciation() (in module skbio.stats.evolve) I identity() (skbio.sequence.SubstitutionMatrix class method) ids (skbio.embedding.Embedding attribute) (skbio.stats.distance.DissimilarityMatrix attribute) ids() (skbio.table.Table method) iloc (skbio.alignment.TabularMSA attribute) ilr() (in module skbio.stats.composition) ilr_inv() (in module skbio.stats.composition) index (skbio.alignment.TabularMSA attribute) index() (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) index_tree() (skbio.tree.TreeNode method) initialize_state() (skbio.workflow.Workflow method) inner() (in module skbio.stats.composition) insert() (skbio.tree.TreeNode method) Interval (class in skbio.metadata) interval_metadata (skbio.metadata.IntervalMetadataMixin attribute) IntervalMetadata (class in skbio.metadata) IntervalMetadataMixin (class in skbio.metadata) inv_simpson() (in module skbio.diversity.alpha) invalidate_caches() (skbio.tree.TreeNode method) IORegistry (class in skbio.io.registry) is_ascii (skbio.sequence.SubstitutionMatrix attribute) is_bifurcating() (skbio.tree.TreeNode method) is_binary_format (skbio.io.registry.Format attribute) is_empty() (skbio.table.Table method) is_reverse_complement() (skbio.sequence.NucleotideMixin method) is_root() (skbio.tree.TreeNode method) is_tip() (skbio.tree.TreeNode method) is_zero_based() (skbio.alignment.AlignmentStructure method) isubsample() (in module skbio.stats) iter() (skbio.table.Table method) iter_contiguous() (skbio.sequence.Sequence method) iter_data() (skbio.table.Table method) iter_kmers() (skbio.sequence.Sequence method) iter_pairwise() (skbio.table.Table method) iter_positions() (skbio.alignment.TabularMSA method) J join() (skbio.alignment.TabularMSA method) K kempton_taylor_q() (in module skbio.diversity.alpha) kmer_distance() (in module skbio.sequence.distance) kmer_frequencies() (skbio.sequence.Sequence method) L lca() (skbio.tree.TreeNode method) length() (skbio.table.Table method) lengths (skbio.alignment.AlignPath attribute) levelorder() (skbio.tree.TreeNode method) list_read_formats() (skbio.io.registry.IORegistry method) list_write_formats() (skbio.io.registry.IORegistry method) lladser_ci() (in module skbio.diversity.alpha) lladser_pe() (in module skbio.diversity.alpha) load() (skbio.metadata.SampleMetadata class method) loc (skbio.alignment.TabularMSA attribute) local_pairwise_align() (in module skbio.alignment) local_pairwise_align_nucleotide() (in module skbio.alignment) local_pairwise_align_protein() (in module skbio.alignment) local_pairwise_align_ssw() (in module skbio.alignment) lower_bound (skbio.metadata.IntervalMetadata attribute) lowercase() (skbio.sequence.Sequence method) lowest_common_ancestor() (skbio.tree.TreeNode method) M majority_rule() (in module skbio.tree) make_identity_substitution_matrix() (in module skbio.alignment) mantel() (in module skbio.stats.distance) margalef() (in module skbio.diversity.alpha) match_frequency() (skbio.sequence.Sequence method) matches() (skbio.sequence.Sequence method) matrix_data (skbio.table.Table attribute) max() (skbio.table.Table method) maxdist() (skbio.tree.TreeNode method) mcintosh_d() (in module skbio.diversity.alpha) mcintosh_e() (in module skbio.diversity.alpha) mean_and_std() (in module skbio.stats.ordination) menhinick() (in module skbio.diversity.alpha) merge() (skbio.metadata.IntervalMetadata method) (skbio.metadata.SampleMetadata method) (skbio.table.Table method) metadata (skbio.metadata.Interval attribute) (skbio.metadata.MetadataMixin attribute) metadata() (skbio.table.Table method) metadata_to_dataframe() (skbio.table.Table method) MetadataColumn (class in skbio.metadata) MetadataMixin (class in skbio.metadata) method (class in skbio.workflow) michaelis_menten_fit() (in module skbio.diversity.alpha) min() (skbio.table.Table method) mismatch_frequency() (skbio.sequence.Sequence method) mismatches() (skbio.sequence.Sequence method) missing_scheme (skbio.metadata.MetadataColumn attribute) module skbio.alignment skbio.diversity skbio.diversity.alpha skbio.diversity.beta skbio.embedding skbio.io skbio.io.format.binary_dm skbio.io.format.biom skbio.io.format.blast6 skbio.io.format.blast7 skbio.io.format.clustal skbio.io.format.embed skbio.io.format.embl skbio.io.format.fasta skbio.io.format.fastq skbio.io.format.genbank skbio.io.format.gff3 skbio.io.format.lsmat skbio.io.format.newick skbio.io.format.ordination skbio.io.format.phylip skbio.io.format.qseq skbio.io.format.sample_metadata skbio.io.format.stockholm skbio.io.format.taxdump skbio.io.registry skbio.io.util skbio.metadata skbio.sequence skbio.sequence.distance skbio.stats skbio.stats.composition skbio.stats.distance skbio.stats.evolve skbio.stats.gradient skbio.stats.ordination skbio.stats.power skbio.table skbio.tree skbio.util skbio.workflow multi_replace() (in module skbio.stats.composition) multiplicative_replacement() (in module skbio.stats.composition) N name (skbio.io.registry.Format attribute) (skbio.metadata.MetadataColumn attribute) (skbio.sequence.GeneticCode attribute) neighbors() (skbio.tree.TreeNode method) nj() (in module skbio.tree) nni() (in module skbio.tree) nnz (skbio.table.Table attribute) non_tips() (skbio.tree.TreeNode method) noncanonical_chars (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) nondegenerate_chars (skbio.sequence.GrammaredSequence attribute) nondegenerates() (skbio.sequence.GrammaredSequence method) nonzero() (skbio.table.Table method) nonzero_counts() (skbio.table.Table method) norm() (skbio.table.Table method) NucleotideMixin (class in skbio.sequence) num_interval_features (skbio.metadata.IntervalMetadata attribute) NumericMetadataColumn (class in skbio.metadata) O observed_chars (skbio.sequence.Sequence attribute) observed_features() (in module skbio.diversity.alpha) observed_node_counts() (skbio.tree.TreeNode method) observed_otus() (in module skbio.diversity.alpha) open() (in module skbio.io.util) open_file() (in module skbio.io.util) open_files() (in module skbio.io.util) optimal_alignment_score (skbio.alignment.AlignmentStructure attribute) OrdinationResults (class in skbio.stats.ordination) osd() (in module skbio.diversity.alpha) P pa() (skbio.table.Table method) PairAlignPath (class in skbio.alignment) paired_subsamples() (in module skbio.stats.power) pairwise_vlr() (in module skbio.stats.composition) partial_beta_diversity() (in module skbio.diversity) partition() (skbio.table.Table method) path() (skbio.tree.TreeNode method) path_dists() (in module skbio.tree) pcoa() (in module skbio.stats.ordination) pcoa_biplot() (in module skbio.stats.ordination) permanova() (in module skbio.stats.distance) permdisp() (in module skbio.stats.distance) permute() (skbio.stats.distance.DistanceMatrix method) perturb() (in module skbio.stats.composition) perturb_inv() (in module skbio.stats.composition) phydiv() (in module skbio.diversity.alpha) pielou_e() (in module skbio.diversity.alpha) plot() (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.ordination.OrdinationResults method) PlottableMixin (class in skbio.util) png (skbio.util.PlottableMixin attribute) pop() (skbio.tree.TreeNode method) positional_metadata (skbio.metadata.PositionalMetadataMixin attribute) PositionalMetadataMixin (class in skbio.metadata) postorder() (skbio.tree.TreeNode method) power() (in module skbio.stats.composition) pre_and_postorder() (skbio.tree.TreeNode method) preorder() (skbio.tree.TreeNode method) Protein (class in skbio.sequence) ProteinEmbedding (class in skbio.embedding) ProteinVector (class in skbio.embedding) prune() (skbio.tree.TreeNode method) pwmantel() (in module skbio.stats.distance) Q query() (skbio.metadata.IntervalMetadata method) query_begin (skbio.alignment.AlignmentStructure attribute) query_end (skbio.alignment.AlignmentStructure attribute) query_sequence (skbio.alignment.AlignmentStructure attribute) R randdm() (in module skbio.stats.distance) rankdata() (skbio.table.Table method) rda() (in module skbio.stats.ordination) read() (in module skbio.io.registry) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.io.registry.IORegistry method) (skbio.metadata.IntervalMetadata method) (skbio.sequence.DNA method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) reader() (skbio.io.registry.Format method) readers (skbio.io.registry.Format attribute) reading_frames (skbio.sequence.GeneticCode attribute) reassign_index() (skbio.alignment.TabularMSA method) reduce() (skbio.table.Table method) redundant_form() (skbio.stats.distance.DissimilarityMatrix method) remove() (skbio.tree.TreeNode method) remove_by_func() (skbio.tree.TreeNode method) remove_deleted() (skbio.tree.TreeNode method) remove_empty() (skbio.table.Table method) remove_format() (skbio.io.registry.IORegistry method) rename() (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.ordination.OrdinationResults method) renyi() (in module skbio.diversity.alpha) replace() (skbio.sequence.Sequence method) requires (class in skbio.workflow) residues (skbio.embedding.ProteinEmbedding attribute) reverse_complement() (skbio.sequence.NucleotideMixin method) reverse_transcribe() (skbio.sequence.RNA method) rf_dists() (in module skbio.tree) RNA (class in skbio.sequence) robbins() (in module skbio.diversity.alpha) root() (skbio.tree.TreeNode method) root_at() (skbio.tree.TreeNode method) root_at_midpoint() (skbio.tree.TreeNode method) root_by_outgroup() (skbio.tree.TreeNode method) S safe_md5() (in module skbio.util) SampleMetadata (class in skbio.metadata) sbp_basis() (in module skbio.stats.composition) scale() (in module skbio.stats.ordination) scores (skbio.sequence.SubstitutionMatrix attribute) Sequence (class in skbio.sequence) sequence (skbio.embedding.SequenceEmbedding attribute) (skbio.embedding.SequenceVector attribute) SequenceEmbedding (class in skbio.embedding) SequenceVector (class in skbio.embedding) set_zero_based() (skbio.alignment.AlignmentStructure method) shannon() (in module skbio.diversity.alpha) shape (skbio.alignment.AlignPath attribute) (skbio.alignment.TabularMSA attribute) (skbio.stats.distance.DissimilarityMatrix attribute) (skbio.table.Table attribute) shear() (skbio.tree.TreeNode method) shuffle() (skbio.tree.TreeNode method) siblings() (skbio.tree.TreeNode method) simpson() (in module skbio.diversity.alpha) simpson_d() (in module skbio.diversity.alpha) simpson_e() (in module skbio.diversity.alpha) singles() (in module skbio.diversity.alpha) size (skbio.stats.distance.DissimilarityMatrix attribute) skbio.alignment module skbio.diversity module skbio.diversity.alpha module skbio.diversity.beta module skbio.embedding module skbio.io module skbio.io.format.binary_dm module skbio.io.format.biom module skbio.io.format.blast6 module skbio.io.format.blast7 module skbio.io.format.clustal module skbio.io.format.embed module skbio.io.format.embl module skbio.io.format.fasta module skbio.io.format.fastq module skbio.io.format.genbank module skbio.io.format.gff3 module skbio.io.format.lsmat module skbio.io.format.newick module skbio.io.format.ordination module skbio.io.format.phylip module skbio.io.format.qseq module skbio.io.format.sample_metadata module skbio.io.format.stockholm module skbio.io.format.taxdump module skbio.io.registry module skbio.io.util module skbio.metadata module skbio.sequence module skbio.sequence.distance module skbio.stats module skbio.stats.composition module skbio.stats.distance module skbio.stats.evolve module skbio.stats.gradient module skbio.stats.ordination module skbio.stats.power module skbio.table module skbio.tree module skbio.util module skbio.workflow module sniff() (in module skbio.io.registry) (skbio.io.registry.IORegistry method) sniffer() (skbio.io.registry.Format method) sniffer_function (skbio.io.registry.Format attribute) sobs() (in module skbio.diversity.alpha) sort() (skbio.alignment.TabularMSA method) (skbio.metadata.IntervalMetadata method) (skbio.table.Table method) sort_order() (skbio.table.Table method) starts (skbio.alignment.AlignPath attribute) states (skbio.alignment.AlignPath attribute) stop_chars (skbio.sequence.Protein attribute) stops() (skbio.sequence.Protein method) StripedSmithWaterman (class in skbio.alignment) strong() (in module skbio.diversity.alpha) suboptimal_alignment_score (skbio.alignment.AlignmentStructure attribute) subsample() (skbio.table.Table method) subsample_counts() (in module skbio.stats) subsample_paired_power() (in module skbio.stats.power) subsample_power() (in module skbio.stats.power) subset() (skbio.tree.TreeNode method) subsets() (skbio.tree.TreeNode method) SubstitutionMatrix (class in skbio.sequence) subtree() (skbio.tree.TreeNode method) sum() (skbio.table.Table method) svd_rank() (in module skbio.stats.ordination) svg (skbio.util.PlottableMixin attribute) T T (skbio.stats.distance.DissimilarityMatrix attribute) Table (class in skbio.table) TabularMSA (class in skbio.alignment) target_begin (skbio.alignment.AlignmentStructure attribute) target_end_optimal (skbio.alignment.AlignmentStructure attribute) target_end_suboptimal (skbio.alignment.AlignmentStructure attribute) target_sequence (skbio.alignment.AlignmentStructure attribute) tip_tip_distances() (skbio.tree.TreeNode method) tips() (skbio.tree.TreeNode method) to_anndata() (skbio.table.Table method) to_array() (skbio.tree.TreeNode method) to_bits() (skbio.alignment.AlignPath method) (skbio.alignment.PairAlignPath method) to_cigar() (skbio.alignment.PairAlignPath method) to_coordinates() (skbio.alignment.AlignPath method) to_data_frame() (skbio.stats.distance.DissimilarityMatrix method) to_dataframe() (skbio.metadata.MetadataColumn method) (skbio.metadata.SampleMetadata method) (skbio.table.Table method) to_definites() (skbio.sequence.GrammaredSequence method) to_dict() (skbio.alignment.TabularMSA method) (skbio.sequence.SubstitutionMatrix method) to_files() (skbio.stats.gradient.CategoryResults method) (skbio.stats.gradient.GradientANOVAResults method) (skbio.stats.gradient.GroupResults method) to_hdf5() (skbio.table.Table method) to_indices() (skbio.alignment.AlignPath method) (skbio.sequence.Sequence method) to_json() (skbio.table.Table method) to_regex() (skbio.sequence.GrammaredSequence method) to_series() (skbio.metadata.MetadataColumn method) (skbio.stats.distance.DistanceMatrix method) to_taxonomy() (skbio.tree.TreeNode method) to_tsv() (skbio.table.Table method) total_length() (skbio.tree.TreeNode method) TrajectoryGradientANOVA (class in skbio.stats.gradient) transcribe() (skbio.sequence.DNA method) transform() (skbio.table.Table method) translate() (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.RNA method) translate_six_frames() (skbio.sequence.DNA method) (skbio.sequence.GeneticCode method) (skbio.sequence.RNA method) transpose() (skbio.stats.distance.DissimilarityMatrix method) (skbio.table.Table method) traverse() (skbio.tree.TreeNode method) tree_basis() (in module skbio.stats.composition) TreeNode (class in skbio.tree) tsallis() (in module skbio.diversity.alpha) type (skbio.metadata.CategoricalMetadataColumn attribute) (skbio.metadata.MetadataColumn attribute) (skbio.metadata.NumericMetadataColumn attribute) U unpack() (skbio.tree.TreeNode method) unpack_by_func() (skbio.tree.TreeNode method) unroot() (skbio.tree.TreeNode method) unrooted_copy() (skbio.tree.TreeNode method) unrooted_deepcopy() (skbio.tree.TreeNode method) unrooted_move() (skbio.tree.TreeNode method) unweighted_unifrac() (in module skbio.diversity.beta) update_ids() (skbio.table.Table method) upgma() (in module skbio.tree) upper_bound (skbio.metadata.IntervalMetadata attribute) V values (skbio.sequence.Sequence attribute) vector (skbio.embedding.EmbeddingVector attribute) vlr() (in module skbio.stats.composition) W weighted_unifrac() (in module skbio.diversity.beta) wildcard_char (skbio.sequence.DNA attribute) (skbio.sequence.GrammaredSequence attribute) (skbio.sequence.Protein attribute) (skbio.sequence.RNA attribute) WindowDifferenceGradientANOVA (class in skbio.stats.gradient) within() (skbio.stats.distance.DissimilarityMatrix method) Workflow (class in skbio.workflow) wrf_dists() (in module skbio.tree) write() (in module skbio.io.registry) (skbio.alignment.TabularMSA method) (skbio.embedding.Embedding method) (skbio.io.registry.IORegistry method) (skbio.metadata.IntervalMetadata method) (skbio.sequence.DNA method) (skbio.sequence.Protein method) (skbio.sequence.RNA method) (skbio.sequence.Sequence method) (skbio.stats.distance.DissimilarityMatrix method) (skbio.stats.ordination.OrdinationResults method) (skbio.table.Table method) (skbio.tree.TreeNode method) writer() (skbio.io.registry.Format method) writers (skbio.io.registry.Format attribute)
