Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X A add_column_from_str() (Columns method) add_feature() (Alignment method) (BasicAnnotationDb method) (DnaSequence method) (GenbankAnnotationDb method) (GffAnnotationDb method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) add_records() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) add_seqs() (AlignedSeqsData method) (Alignment method) (SequenceCollection method) align_len (AlignedSeqsData property) Aligned (class in cogent3.core.alignment) AlignedSeqsData (class in cogent3.core.alignment) Alignment (class in cogent3.core.alignment) alignment_quality() (Alignment method) alphabet (AlignedSeqsData property) (MolType property) (SeqView attribute) ancestors() (PhyloNode method) annotate_matches_to() (Aligned method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) annotation_db (Aligned property) (Alignment property) (DnaSequence property) (ProteinSequence property) (RnaSequence property) (SequenceCollection property) annotation_offset (DnaSequence property) (ProteinSequence property) (RnaSequence property) anticodons (GeneticCode attribute) append() (PhyloNode method) appended() (Table method) apply_pssm() (SequenceCollection method) apply_scaled_gaps() (Alignment method) array (Columns property) (Table property) array_positions (Alignment property) array_seqs (Alignment property) array_to_bytes() (CharAlphabet method) array_value (SeqView property) as_bytes() (CharAlphabet method) as_one_span() (Feature method) ascii_art() (PhyloNode method) B balanced() (PhyloNode method) BasicAnnotationDb (class in cogent3.core.annotation_db) bifurcating() (PhyloNode method) biotype (Feature property) biotype_counts() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) bytes_value (SeqView property) C can_match() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) can_mispair() (DnaSequence method) (MolType method) (RnaSequence method) can_pair() (DnaSequence method) (MolType method) (RnaSequence method) CharAlphabet (class in cogent3.core.alphabet) child_parent_map() (PhyloNode method) children (PhyloNode attribute) clear() (Columns method) close() (BasicAnnotationDb method) (DataStoreSqlite method) (GenbankAnnotationDb method) (GffAnnotationDb method) codons (GeneticCode attribute) coevolution() (Alignment method) cogent.app cogent.db.ensembl cogent.db.eutils cogent.maths.unifrac cogent.motif cogent.seqsim cogent.struct Columns (class in cogent3.core.table) compare_by_names() (PhyloNode method) compare_by_subsets() (PhyloNode method) compare_name() (PhyloNode method) compatible() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) complement() (DnaSequence method) (MolType method) (RnaSequence method) completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) completed members convert_seq_array_to() (CharAlphabet method) copy() (AlignedSeqsData method) (Alignment method) (DnaSequence method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SeqView method) copy_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) count() (CharAlphabet method) (DnaSequence method) (KmerAlphabet method) (ProteinSequence method) (RnaSequence method) (SenseCodonAlphabet method) (Table method) count_ambiguous() (DnaSequence method) (ProteinSequence method) (RnaSequence method) count_ambiguous_per_seq() (Alignment method) (SequenceCollection method) count_degenerate() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) count_distinct() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) count_gaps() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) count_gaps_per_pos() (Alignment method) count_gaps_per_seq() (Alignment method) count_kmers() (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) count_unique() (Table method) count_variants() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) counts() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) counts_per_pos() (Alignment method) counts_per_seq() (Alignment method) (SequenceCollection method) cross_join() (Table method) D data (Aligned property) data store data_store (DataMember property) DataMember (class in cogent3.app.data_store) DataStoreDirectory (class in cogent3.app.data_store) DataStoreSqlite (class in cogent3.app.sqlite_data_store) db (BasicAnnotationDb property) (DataStoreSqlite property) (GenbankAnnotationDb property) (GffAnnotationDb property) deepcopy() (Alignment method) (PhyloNode method) define_app() (in module cogent3.app.composable) degap() (Alignment method) (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) degen_alphabet (MolType property) degen_gapped_alphabet (MolType property) degenerate_from_seq() (MolType method) descendant_array() (PhyloNode method) describe (BasicAnnotationDb property) (DataStoreDirectory property) (DataStoreSqlite property) (GenbankAnnotationDb property) (GffAnnotationDb property) (ReadOnlyDataStoreZipped property) deserialise_object() (in module cogent3.util.deserialise) diff() (DnaSequence method) (ProteinSequence method) (RnaSequence method) disambiguate() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) distance() (DnaSequence method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) distance_matrix() (Alignment method) (SequenceCollection method) distinct_values() (Table method) DnaSequence (class in cogent3.core.sequence) dotplot() (Alignment method) (SequenceCollection method) drop_duplicated_seqs() (Alignment method) (SequenceCollection method) drop_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) duplicated_seqs() (Alignment method) (SequenceCollection method) E entropy_per_pos() (Alignment method) entropy_per_seq() (Alignment method) (SequenceCollection method) extend() (PhyloNode method) F Feature (class in cogent3.core.annotation) filtered() (Alignment method) (Table method) filtered_by_column() (Table method) FilteringParser (class in cogent3.parse.table) format (Table property) format_column() (Table method) frac_diff() (DnaSequence method) (ProteinSequence method) (RnaSequence method) frac_diff_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) frac_diff_non_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) frac_same() (DnaSequence method) (ProteinSequence method) (RnaSequence method) frac_same_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) frac_same_non_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) frac_similar() (DnaSequence method) (ProteinSequence method) (RnaSequence method) from_dict() (BasicAnnotationDb class method) (GenbankAnnotationDb class method) (GffAnnotationDb class method) from_index() (KmerAlphabet method) (SenseCodonAlphabet method) from_indices() (CharAlphabet method) (KmerAlphabet method) (SenseCodonAlphabet method) from_map_and_aligned_data_view() (Aligned class method) from_map_and_seq() (Aligned class method) from_names_and_array() (AlignedSeqsData class method) from_rich_dict() (Alignment class method) (CharAlphabet class method) (DnaSequence class method) (KmerAlphabet class method) (ProteinSequence class method) (RnaSequence class method) (SenseCodonAlphabet class method) (SequenceCollection class method) from_seqs() (AlignedSeqsData class method) from_seqs_and_gaps() (AlignedSeqsData class method) G gap_char (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) gap_index (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) gap_indices() (DnaSequence method) (ProteinSequence method) (RnaSequence method) gap_vector() (Aligned method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) gapped_alphabet (MolType property) gapped_by_map() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) gapped_by_map_motif_iter() (DnaSequence method) (ProteinSequence method) (RnaSequence method) gapped_by_map_segment_iter() (DnaSequence method) (ProteinSequence method) (RnaSequence method) gapped_missing_alphabet (MolType property) gapped_seq (Aligned property) gaps (MolType property) GenbankAnnotationDb (class in cogent3.core.annotation_db) GeneticCode (class in cogent3.core.genetic_code) get() (Columns method) get_alphabet() (GeneticCode method) get_ambiguous_positions() (Alignment method) (SequenceCollection method) get_children() (Feature method) get_columns() (Table method) get_connecting_edges() (PhyloNode method) get_connecting_node() (PhyloNode method) get_coordinates() (Feature method) get_css_style() (MolType method) get_degapped_relative_to() (Alignment method) get_degenerate_positions() (MolType method) get_drawable() (Alignment method) (DnaSequence method) (Feature method) (ProteinSequence method) (RnaSequence method) get_drawables() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_edge_names() (PhyloNode method) get_edge_vector() (PhyloNode method) get_feature_children() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_feature_parent() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_features() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) get_features_matching() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_figure() (PhyloNode method) get_gap_array() (Alignment method) get_gapped_seq() (Alignment method) get_gapped_seq_array() (AlignedSeqsData method) get_gapped_seq_bytes() (AlignedSeqsData method) get_gapped_seq_str() (AlignedSeqsData method) get_gaps() (AlignedSeqsData method) get_hash() (AlignedSeqsData method) get_identical_sets() (Alignment method) (SequenceCollection method) get_in_motif_size() (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_kmer_alphabet() (CharAlphabet method) get_kmers() (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_lengths() (Alignment method) (SequenceCollection method) get_max_tip_tip_distance() (PhyloNode method) get_motif_probs() (Alignment method) (SequenceCollection method) get_name() (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_neighbours_except() (PhyloNode method) get_newick() (PhyloNode method) get_node_matching_name() (PhyloNode method) get_node_names() (PhyloNode method) get_nodes_dict() (PhyloNode method) get_param_value() (PhyloNode method) get_parent() (Feature method) get_pos_range() (AlignedSeqsData method) get_position_indices() (Alignment method) get_positions() (AlignedSeqsData method) get_projected_feature() (Alignment method) get_projected_features() (Alignment method) get_records_matching() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_root() (PhyloNode method) get_row_indices() (Table method) get_seq() (Alignment method) (SequenceCollection method) get_seq_array() (AlignedSeqsData method) get_seq_bytes() (AlignedSeqsData method) get_seq_length() (AlignedSeqsData method) get_seq_names_if() (Alignment method) (SequenceCollection method) get_seq_str() (AlignedSeqsData method) get_similar() (Alignment method) (SequenceCollection method) get_slice() (Feature method) get_sub_tree() (PhyloNode method) get_subset() (CharAlphabet method) get_tip_names() (PhyloNode method) get_translation() (Alignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) get_type() (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_ungapped() (AlignedSeqsData method) get_view() (AlignedSeqsData method) GffAnnotationDb (class in cogent3.core.annotation_db) H has_ambiguity() (MolType method) has_terminal_stop() (Alignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) head() (Table method) header (Table property) I ID (GeneticCode attribute) index() (CharAlphabet method) (KmerAlphabet method) (SenseCodonAlphabet method) index_in_parent() (PhyloNode method) index_name (Columns property) (Table property) info (DnaSequence attribute) (ProteinSequence attribute) (RnaSequence attribute) information_plot() (Alignment method) inner_join() (Table method) insert() (PhyloNode method) is_ambiguity() (MolType method) is_annotated() (DnaSequence method) (ProteinSequence method) (RnaSequence method) is_compatible_alphabet() (MolType method) is_degenerate() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_gapped() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_nucleic (MolType property) is_ragged() (Alignment method) (SequenceCollection method) is_reversed (SeqView property) is_root() (PhyloNode method) is_start() (GeneticCode method) is_stop() (GeneticCode method) is_strict() (DnaSequence method) (ProteinSequence method) (RnaSequence method) is_tip() (PhyloNode method) is_valid() (CharAlphabet method) (DnaSequence method) (KmerAlphabet method) (MolType method) (ProteinSequence method) (RnaSequence method) (SenseCodonAlphabet method) isroot() (PhyloNode method) istip() (PhyloNode method) items() (Columns method) iter_alphabets() (MolType method) iter_kmers() (DnaSequence method) (ProteinSequence method) (RnaSequence method) iter_nontips() (PhyloNode method) iter_positions() (Alignment method) iter_rows() (Columns method) iter_seqs() (Alignment method) (SequenceCollection method) iter_tips() (PhyloNode method) iupac_consensus() (Alignment method) J joined() (Table method) K keys() (Columns method) KmerAlphabet (class in cogent3.core.alphabet) L label (MolType property) ladderise() (PhyloNode method) ladderize() (PhyloNode method) last_common_ancestor() (PhyloNode method) lca() (PhyloNode method) legend (Table property) length (PhyloNode attribute) levelorder() (PhyloNode method) limit (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) lin_rajan_moret() (PhyloNode method) load_aligned_seqs() (in module cogent3.__init__) load_seq() (in module cogent3.__init__) load_unaligned_seqs() (in module cogent3.__init__) lock() (DataStoreSqlite method) locked (DataStoreSqlite property) logs (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) lowest_common_ancestor() (PhyloNode method) M majority_consensus() (Alignment method) make_feature() (Aligned method) (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) make_indexes() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) make_seq() (in module cogent3.__init__) (MolType method) make_tree_array() (PhyloNode method) map (Aligned property) (Feature property) matching_ref() (Alignment method) matching_rules (MolType property) matrix_distance() (DnaSequence method) (ProteinSequence method) (RnaSequence method) max_tip_tip_distance() (PhyloNode method) md5 (DataMember property) md5() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) members (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) missing_char (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) missing_index (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) mode (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) modified (Alignment property) (SequenceCollection property) moltype (Aligned property) (CharAlphabet property) MolType (class in cogent3.core.moltype) moltype (DnaSequence attribute) (GeneticCode attribute) (KmerAlphabet property) (ProteinSequence attribute) (RnaSequence attribute) (SenseCodonAlphabet property) most_degen_alphabet() (MolType method) motif_len (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) multifurcating() (PhyloNode method) must_pair() (DnaSequence method) (RnaSequence method) mw() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) N name (Aligned property) (DnaSequence attribute) (Feature property) (GeneticCode attribute) (PhyloNode attribute) (ProteinSequence attribute) (RnaSequence attribute) name_loaded (PhyloNode attribute) name_map (Alignment property) (SequenceCollection property) name_unnamed_nodes() (PhyloNode method) names (AlignedSeqsData property) (Alignment property) (SequenceCollection property) ncbi_code_sequence (GeneticCode attribute) ncbi_start_codon_map (GeneticCode attribute) no_degenerates() (Alignment method) non_tip_children() (PhyloNode method) nontips() (PhyloNode method) normalized() (Table method) not_completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) num_canonical (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) num_matches() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) num_seqs (Alignment property) (SequenceCollection property) O offset (AlignedSeqsData property) (SeqView property) omit_bad_seqs() (Alignment method) omit_gap_pos() (Alignment method) open_data_store() order (Columns property) P pad_seqs() (Alignment method) (SequenceCollection method) params (PhyloNode attribute) parent (Feature property) (PhyloNode property) (SeqView attribute) parent_coordinates() (Aligned method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) parent_coords() (SeqView method) parent_len (SeqView property) parent_offset (SeqView property) parse_out_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) parse_token() (PhyloNode static method) PhyloNode (class in cogent3.core.tree) pop() (Columns method) (PhyloNode method) popitem() (Columns method) positions (Alignment property) postorder() (PhyloNode method) pre_and_postorder() (PhyloNode method) preorder() (PhyloNode method) probs_per_pos() (Alignment method) probs_per_seq() (Alignment method) (SequenceCollection method) ProteinSequence (class in cogent3.core.sequence) prune() (PhyloNode method) Q quick_tree() (Alignment method) R random_disambiguate() (MolType method) rc() (Alignment method) (DnaSequence method) (MolType method) (RnaSequence method) (SequenceCollection method) read() (DataMember method) (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) ReadOnlyDataStoreZipped (class in cogent3.app.data_store) reassign_names() (PhyloNode method) record_type (DataStoreSqlite property) register_datastore_reader() (in module cogent3.app.io) register_deserialiser (class in cogent3.util.deserialise) remapped_to() (Feature method) remove() (PhyloNode method) remove_deleted() (PhyloNode method) remove_node() (PhyloNode method) rename_seqs() (Alignment method) (SequenceCollection method) renamed_nodes() (PhyloNode method) renamed_seqs() (Alignment method) (SequenceCollection method) replace_annotation_db() (Aligned method) (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) resolve_ambiguity() (MolType method) resolved_ambiguities() (DnaSequence method) (ProteinSequence method) (RnaSequence method) reverse_complement() (Alignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) reversed (Feature property) reversed_seqs (AlignedSeqsData property) RnaSequence (class in cogent3.core.sequence) root_at_midpoint() (PhyloNode method) rooted() (PhyloNode method) rooted_at() (PhyloNode method) rooted_with_tip() (PhyloNode method) S same_shape() (PhyloNode method) same_topology() (PhyloNode method) sample() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) sense_codons (GeneticCode property) SenseCodonAlphabet (class in cogent3.core.alphabet) separation() (PhyloNode method) seq (Aligned property) seqid (Feature property) (SeqView property) seqlogo() (Alignment method) seqs (Alignment property) (SequenceCollection property) SequenceCollection (class in cogent3.core.alignment) SeqView (class in cogent3.core.sequence) set_param_value() (PhyloNode method) set_repr_policy() (SequenceCollection method) (Table method) setdefault() (Columns method) shadow() (Feature method) shape (Table property) shuffle() (DnaSequence method) (ProteinSequence method) (RnaSequence method) siblings() (PhyloNode method) sixframes() (GeneticCode method) slice_record (SeqView property) slice_with_map() (Aligned method) sliding_windows() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) sorted() (PhyloNode method) (Table method) source (DataStoreDirectory property) (DataStoreSqlite property) (PhyloNode property) (ReadOnlyDataStoreZipped property) space (Table property) start_codons (GeneticCode property) stop_codons (GeneticCode property) storage (Alignment property) (SequenceCollection property) store_suffix (DataStoreSqlite attribute) str_value (SeqView property) strand_symmetric_motifs() (MolType method) strand_symmetry() (Alignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) strip_bad() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) strip_bad_and_gaps() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) strip_degenerate() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) StrOrBool (BasicAnnotationDb attribute) (GenbankAnnotationDb attribute) (GffAnnotationDb attribute) subset() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) (PhyloNode method) subsets() (PhyloNode method) sum_columns() (Table method) sum_rows() (Table method) summary_logs (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) summary_not_completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) summed() (Table method) support (PhyloNode attribute) synonyms (GeneticCode property) T Table (class in cogent3.core.table) table_names (BasicAnnotationDb property) (GenbankAnnotationDb property) (GffAnnotationDb property) tail() (Table method) take_columns() (Columns method) take_positions() (Alignment method) take_positions_if() (Alignment method) take_seqs() (Alignment method) (SequenceCollection method) take_seqs_if() (Alignment method) (SequenceCollection method) tip_children() (PhyloNode method) tip_to_root_distances() (PhyloNode method) tip_to_tip_distances() (PhyloNode method) tips() (PhyloNode method) tips_within_distance() (PhyloNode method) title (Table property) to_alphabet() (AlignedSeqsData method) to_array() (DnaSequence method) (ProteinSequence method) (RnaSequence method) to_categorical() (Table method) to_csv() (Table method) to_dict() (Alignment method) (Columns method) (Feature method) (SequenceCollection method) (Table method) to_dna() (Alignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) to_fasta() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) to_html() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) (Table method) to_index() (KmerAlphabet method) (SenseCodonAlphabet method) to_indices() (CharAlphabet method) (KmerAlphabet method) (SenseCodonAlphabet method) to_json() (Alignment method) (BasicAnnotationDb method) (CharAlphabet method) (DnaSequence method) (GenbankAnnotationDb method) (GffAnnotationDb method) (KmerAlphabet method) (MolType method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SenseCodonAlphabet method) (SequenceCollection method) (Table method) to_latex() (Table method) to_list() (Table method) to_markdown() (Table method) to_moltype() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) to_pandas() (Table method) to_phylip() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) to_plotly() (Table method) to_pretty() (Alignment method) to_regex() (GeneticCode method) (MolType method) to_rich_dict() (Alignment method) (BasicAnnotationDb method) (CharAlphabet method) (Columns method) (DnaSequence method) (GenbankAnnotationDb method) (GffAnnotationDb method) (KmerAlphabet method) (MolType method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SenseCodonAlphabet method) (SequenceCollection method) (Table method) to_rna() (Alignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) to_rst() (Table method) to_string() (Table method) to_table() (GeneticCode method) to_tsv() (Table method) total_descending_branch_length() (PhyloNode method) total_length() (PhyloNode method) translate() (GeneticCode method) transposed() (Table method) tree_distance() (PhyloNode method) trim_stop_codon() (DnaSequence method) (RnaSequence method) trim_stop_codons() (Alignment method) (SequenceCollection method) TSeqOrAlignOther (Feature attribute) U union() (BasicAnnotationDb method) (Feature method) (GenbankAnnotationDb method) (GffAnnotationDb method) unique_id (DataMember property) unlock() (DataStoreSqlite method) unrooted() (PhyloNode method) unrooted_deepcopy() (PhyloNode method) update() (BasicAnnotationDb method) (Columns method) (GenbankAnnotationDb method) (GffAnnotationDb method) update_record_spans() (GffAnnotationDb method) V validate() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) values() (Columns method) variable_positions() (AlignedSeqsData method) (Alignment method) W with_gap_motif() (CharAlphabet method) (KmerAlphabet method) (SenseCodonAlphabet method) with_masked_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) with_new_column() (Table method) with_new_header() (Table method) with_offset() (SeqView method) with_termini_unknown() (DnaSequence method) (ProteinSequence method) (RnaSequence method) without_lost_spans() (Feature method) write() (Alignment method) (BasicAnnotationDb method) (DataStoreDirectory method) (DataStoreSqlite method) (GenbankAnnotationDb method) (GffAnnotationDb method) (PhyloNode method) (ReadOnlyDataStoreZipped method) (SequenceCollection method) (Table method) write_log() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) write_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) X xattr (Feature property)
