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 absolute_position() (SliceRecord method) 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) (SeqsData method) (SequenceCollection method) align_len (AlignedSeqsData property) Aligned (class in cogent3.core.new_alignment) AlignedDataView (class in cogent3.core.new_alignment) AlignedSeqsData (class in cogent3.core.new_alignment) Alignment (class in cogent3.core.new_alignment) alignment_quality() (Alignment method) alphabet (AlignedDataView attribute) (AlignedSeqsData property) (MolType property) (SeqDataView attribute) (SeqsData property) (SeqView attribute) ambiguities (MolType attribute) ancestors() (PhyloNode method) annotate_from_gff() (DnaSequence method) (ProteinSequence method) (RnaSequence 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() (Alignment method) (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 (AlignedDataView property) (SeqDataView property) (SeqView property) as_bytes() (CharAlphabet method) as_one_span() (Feature method) ascii_art() (PhyloNode method) available_apps() (in module cogent3.__init__) available_codes() (in module cogent3.__init__) available_models() (in module cogent3.__init__) available_moltypes() (in module cogent3.__init__) 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 (AlignedDataView property) (SeqDataView property) (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.new_alphabet) child_groups() (PhyloNode method) child_parent_map() (PhyloNode method) clear() (Columns method) close() (BasicAnnotationDb method) (DataStoreSqlite method) (GenbankAnnotationDb method) (GffAnnotationDb method) codons (GeneticCode attribute) coerce_to (MolType attribute) coevolution() (Alignment method) cogent.app cogent.db.ensembl cogent.db.eutils cogent.maths.unifrac cogent.motif cogent.seqsim cogent.struct colors (MolType attribute) Columns (class in cogent3.core.table) compare_by_names() (PhyloNode method) compare_by_subsets() (PhyloNode method) compare_by_tip_distances() (PhyloNode method) compare_name() (PhyloNode method) compatible() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) complement() (DnaSequence method) (MolType method) (RnaSequence method) complements (MolType attribute) completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) completed members convert_seq_array_to() (CharAlphabet method) copy() (AlignedDataView method) (AlignedSeqsData method) (Alignment method) (DnaSequence method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SeqDataView method) (SeqsData method) (SeqView method) (SliceRecord method) copy_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) copy_topology() (PhyloNode 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_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.new_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) (SeqsData class method) from_seqs_and_gaps() (AlignedSeqsData class method) G gap (MolType attribute) 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_array_value (AlignedDataView 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_bytes_value (AlignedDataView property) gapped_seq (Aligned property) gapped_str_value (AlignedDataView property) gaps (MolType property) GenbankAnnotationDb (class in cogent3.core.annotation_db) GeneticCode (class in cogent3.core.new_genetic_code) get() (Columns method) get_alphabet() (GeneticCode method) get_ambiguous_positions() (Alignment method) (SequenceCollection method) get_children() (Feature method) get_code() (in module cogent3.__init__) 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_distances() (PhyloNode 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_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_model() (in module cogent3.__init__) get_moltype() (in module cogent3.__init__) get_motif_len() (CharAlphabet method) get_motif_probs() (Alignment method) (SequenceCollection method) get_name() (DnaSequence method) (ProteinSequence method) (RnaSequence 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_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) (SeqsData method) get_seq_bytes() (AlignedSeqsData method) (SeqsData method) get_seq_length() (AlignedSeqsData method) (SeqsData method) get_seq_names_if() (Alignment method) (SequenceCollection method) get_seq_str() (AlignedSeqsData method) (SeqsData method) get_seq_view() (AlignedDataView 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) (SeqsData method) get_word_alphabet() (CharAlphabet method) get_xml() (PhyloNode 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 (AlignedDataView property) (SeqDataView property) (SeqView property) (SliceRecord 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.new_alphabet) L label (MolType property) last_common_ancestor() (PhyloNode method) lca() (PhyloNode method) legend (Table property) length (PhyloNode property) levelorder() (PhyloNode method) limit (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) lin_rajan_moret() (PhyloNode method) load_aligned_seqs() (in module cogent3.__init__) load_annotations() (in module cogent3.__init__) load_delimited() (in module cogent3.__init__) load_seq() (in module cogent3.__init__) load_table() (in module cogent3.__init__) load_tree() (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_aligned_seqs() (in module cogent3.__init__) make_array_seq() (MolType 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_table() (in module cogent3.__init__) make_tree() (in module cogent3.__init__) make_tree_array() (PhyloNode method) make_unaligned_seqs() (in module cogent3.__init__) map (Aligned property) (AlignedDataView 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 (MolType attribute) missing_char (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) missing_index (CharAlphabet property) (KmerAlphabet property) (SenseCodonAlphabet property) mode (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) moltype (Aligned property) (CharAlphabet property) MolType (class in cogent3.core.new_moltype) moltype (DnaSequence attribute) (GeneticCode attribute) (KmerAlphabet property) (ProteinSequence attribute) (RnaSequence attribute) (SenseCodonAlphabet property) monomers (MolType attribute) 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) mw_calculator (MolType attribute) N name (Aligned property) (DnaSequence attribute) (Feature property) (GeneticCode attribute) (MolType attribute) (ProteinSequence attribute) (RnaSequence attribute) name_map (Alignment property) (SequenceCollection property) name_unnamed_nodes() (PhyloNode method) named_seqs (Alignment property) (SequenceCollection property) names (AlignedSeqsData property) (Alignment property) (SeqsData 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 (AlignedDataView property) (AlignedSeqsData property) (SeqDataView property) (SeqsData property) (SeqView property) (SliceRecord property) omit_bad_seqs() (Alignment method) omit_gap_pos() (Alignment method) open_() (in module cogent3.__init__) open_data_store() (in module cogent3.__init__) order (Columns property) P pad_seqs() (Alignment method) (SequenceCollection method) pairing_rules (MolType attribute) parent (AlignedDataView attribute) (Feature property) (PhyloNode property) (SeqDataView attribute) (SeqView attribute) parent_coordinates() (Aligned method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) parent_len (AlignedDataView property) (SeqDataView property) (SeqView property) (SliceRecord property) parent_seq_coords() (AlignedDataView method) parent_start (SliceRecord property) parent_stop (SliceRecord property) parse_out_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) parse_token() (PhyloNode static method) PhyloNode (class in cogent3.core.tree) plus_start (SliceRecord property) plus_step (SliceRecord property) plus_stop (SliceRecord property) 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.new_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) relative_position() (SliceRecord method) remapped_to() (Feature method) remove() (PhyloNode method) remove_deleted() (PhyloNode method) remove_node() (PhyloNode method) rename_seqs() (Alignment method) (SequenceCollection method) replace_annotation_db() (DnaSequence method) (ProteinSequence method) (RnaSequence method) replace_seqs() (Alignment 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) (SeqsData property) RnaSequence (class in cogent3.core.new_sequence) root() (PhyloNode method) 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) scale_branch_lengths() (PhyloNode method) sense_codons (GeneticCode property) SenseCodonAlphabet (class in cogent3.core.new_alphabet) separation() (PhyloNode method) seq (Aligned property) SeqDataView (class in cogent3.core.new_alignment) seqid (AlignedDataView property) (Feature property) (SeqDataView property) (SeqView property) seqlogo() (Alignment method) seqs (Alignment property) (SequenceCollection property) SeqsData (class in cogent3.core.new_alignment) SequenceCollection (class in cogent3.core.new_alignment) SeqView (class in cogent3.core.new_sequence) set_max_tip_tip_distance() (PhyloNode method) set_param_value() (PhyloNode method) set_repr_policy() (Alignment method) (SequenceCollection method) (Table method) set_tip_distances() (PhyloNode 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 (AlignedDataView property) (SeqDataView property) (SeqView property) slice_with_map() (Aligned method) SliceRecord (class in cogent3.core.new_sequence) 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 (SliceRecord attribute) start_codons (GeneticCode property) step (SliceRecord attribute) stop (SliceRecord attribute) stop_codons (GeneticCode property) storage (Alignment property) (SequenceCollection property) store_suffix (DataStoreSqlite attribute) str_value (AlignedDataView property) (SeqDataView property) (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) 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) (SeqsData 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) (SeqDataView method) (SequenceCollection method) (SliceRecord 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) to_type() (Alignment method) total_descending_branch_length() (PhyloNode method) total_length() (PhyloNode method) translate() (GeneticCode method) transposed() (Table method) traverse() (PhyloNode method) tree_distance() (PhyloNode method) trim_stop_codon() (DnaSequence method) (RnaSequence method) trim_stop_codons() (Alignment method) (SequenceCollection method) 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() (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() (AlignedDataView method) (SeqDataView method) (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)
