Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W 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_from_ref_aln() (Alignment method) (ArrayAlignment method) add_note() (Alphabet.AlphabetError method) add_records() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) add_seqs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) Alignment (class in cogent3.core.alignment) alignment_quality() (Alignment method) (ArrayAlignment method) alphabet (ArrayAlignment attribute) Alphabet (class in cogent3.core.alphabet) Alphabet.AlphabetError ancestors() (PhyloNode method) annotate_from_gff() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) annotate_matches_to() (DnaSequence method) (ProteinSequence method) (RnaSequence method) annotation_db (Alignment property) (ArrayAlignment property) (DnaSequence property) (ProteinSequence property) (RnaSequence property) (SequenceCollection property) annotation_offset (DnaSequence property) (ProteinSequence property) (RnaSequence property) append() (PhyloNode method) appended() (Table method) apply_pssm() (Alignment method) (ArrayAlignment method) (SequenceCollection method) args (Alphabet.AlphabetError attribute) array (Columns property) (Table property) ArrayAlignment (class in cogent3.core.alignment) 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) blocks (GeneticCode property) C can_match() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) can_mismatch() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) can_mispair() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) can_pair() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) changes() (GeneticCode method) child_groups() (PhyloNode method) child_parent_map() (PhyloNode method) clear() (Columns method) close() (BasicAnnotationDb method) (DataStoreSqlite method) (GenbankAnnotationDb method) (GffAnnotationDb method) codon_alphabet (DnaSequence attribute) (RnaSequence attribute) coerce_str() (MolType method) coevolution() (Alignment method) (ArrayAlignment method) cogent.app, [1] cogent.db.ensembl, [1] cogent.db.eutils, [1] cogent.maths.unifrac, [1] cogent.motif, [1] cogent.seqsim, [1] cogent.struct, [1] cogent3.util.misc Columns (class in cogent3.util.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) (ProteinSequence method) (RnaSequence method) completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) completed members copy() (Alignment method) (ArrayAlignment method) (DnaSequence method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) copy_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) copy_topology() (PhyloNode method) count() (Alphabet method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (Table 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) (ArrayAlignment method) count_gaps_per_seq() (Alignment method) (ArrayAlignment method) count_unique() (Table method) counts() (Alignment method) (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) counts_per_pos() (Alignment method) (ArrayAlignment method) counts_per_seq() (Alignment method) (ArrayAlignment method) (SequenceCollection method) cross_join() (Table method) D 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) (ArrayAlignment method) (PhyloNode method) (SequenceCollection method) default_gap (Alignment attribute) (ArrayAlignment attribute) define_app() (in module cogent3.app.composable) degap() (Alignment method) (ArrayAlignment method) (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) 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) (ArrayAlignment method) (SequenceCollection method) distinct_values() (Table method) DnaSequence (class in cogent3.core.sequence) dotplot() (Alignment method) (ArrayAlignment method) (SequenceCollection method) drop_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) E entropy_per_pos() (Alignment method) (ArrayAlignment method) entropy_per_seq() (Alignment method) (ArrayAlignment method) (SequenceCollection method) extend() (PhyloNode method) F Feature (class in cogent3.core.annotation) filtered() (Alignment method) (ArrayAlignment method) (Table method) filtered_by_column() (Table method) FilteringParser (class in cogent3.parse.table) first_degenerate() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) first_gap() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) first_invalid() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) first_non_strict() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) first_not_in_alphabet() (MolType method) 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_indices() (Alphabet method) G gap_chars (Alignment attribute) (ArrayAlignment attribute) gap_indices() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) gap_maps() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) gap_vector() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) 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) 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) (ArrayAlignment 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) (ArrayAlignment 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) (ArrayAlignment method) get_gap_motif() (Alphabet method) get_gapped_seq() (Alignment method) (ArrayAlignment method) get_identical_sets() (Alignment method) (ArrayAlignment method) (SequenceCollection method) get_in_motif_size() (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_kmers() (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_lengths() (Alignment method) (ArrayAlignment 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() (Alphabet method) get_motif_probs() (Alignment method) (ArrayAlignment 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) (ArrayAlignment method) get_projected_feature() (Alignment method) get_projected_features() (Alignment method) get_records_matching() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_row_indices() (Table method) get_seq() (Alignment method) (ArrayAlignment method) (SequenceCollection method) get_seq_indices() (Alignment method) (ArrayAlignment method) (SequenceCollection method) get_similar() (Alignment method) (ArrayAlignment method) (SequenceCollection method) get_slice() (Feature method) get_stop_indices() (GeneticCode method) get_sub_alignment() (ArrayAlignment method) get_sub_tree() (PhyloNode method) get_subset() (Alphabet method) get_tip_names() (PhyloNode method) get_translation() (Alignment method) (ArrayAlignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) get_type() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) get_word_alphabet() (Alphabet method) get_xml() (PhyloNode method) GffAnnotationDb (class in cogent3.core.annotation_db) H has_terminal_stop() (Alignment method) (ArrayAlignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) head() (Table method) header (Table property) I includes_gap_motif() (Alphabet method) index() (Alphabet method) index_in_parent() (PhyloNode method) index_name (Columns property) (Table property) information_plot() (Alignment method) (ArrayAlignment method) inner_join() (Table method) insert() (PhyloNode method) is_ambiguity() (MolType method) is_annotated() (DnaSequence method) (ProteinSequence method) (RnaSequence method) is_array (Alignment attribute) (ArrayAlignment attribute) (SequenceCollection attribute) is_compatible_alphabet() (MolType method) is_degenerate() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_gap() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_gapped() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_ragged() (Alignment method) (ArrayAlignment method) (SequenceCollection method) is_root() (PhyloNode method) is_start() (GeneticCode method) is_stop() (GeneticCode method) is_strict() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_tip() (PhyloNode method) is_valid() (Alphabet method) (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) isroot() (PhyloNode method) istip() (PhyloNode method) items() (Columns method) iter_kmers() (DnaSequence method) (ProteinSequence method) (RnaSequence method) iter_nontips() (PhyloNode method) iter_positions() (Alignment method) (ArrayAlignment method) iter_rows() (Columns method) iter_selected() (Alignment method) (ArrayAlignment method) (SequenceCollection method) iter_seqs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) iter_tips() (PhyloNode method) iupac_consensus() (Alignment method) (ArrayAlignment method) J joined() (Table method) K keys() (Columns method) L 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) line_wrap (DnaSequence attribute) (ProteinSequence attribute) (RnaSequence attribute) 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) (ArrayAlignment method) make_aligned_seqs() (in module cogent3.__init__) make_array_seq() (MolType method) make_feature() (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 (Feature property) matching_ref() (Alignment method) (ArrayAlignment method) 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) mode (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) moltype (Alignment attribute) (Alphabet property) (ArrayAlignment attribute) MolType (class in cogent3.core.moltype) moltype (DnaSequence attribute) (ProteinSequence attribute) (RnaSequence attribute) (SequenceCollection attribute) multifurcating() (PhyloNode method) must_match() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) must_pair() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) mw() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) N name (Feature property) name_unnamed_nodes() (PhyloNode method) named_seqs (Alignment property) (ArrayAlignment property) (SequenceCollection property) no_degenerates() (Alignment method) (ArrayAlignment method) non_tip_children() (PhyloNode method) nontips() (PhyloNode method) normalized() (Table method) not_completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) num_matches() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) num_seqs (Alignment property) (ArrayAlignment property) (SequenceCollection property) O omit_bad_seqs() (Alignment method) (ArrayAlignment method) omit_gap_pos() (Alignment method) (ArrayAlignment method) omit_gap_runs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) omit_gap_seqs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) open_() (in module cogent3.__init__) open_data_store() (in module cogent3.__init__) order (Columns property) P pad_seqs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) parent (Feature property) (PhyloNode property) parent_coordinates() (DnaSequence method) (ProteinSequence method) (RnaSequence method) parse_out_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) PhyloNode (class in cogent3.core.tree) pop() (Columns method) (PhyloNode method) popitem() (Columns method) positions (Alignment property) (ArrayAlignment property) possibilities() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) postorder() (PhyloNode method) pre_and_postorder() (PhyloNode method) preorder() (PhyloNode method) probs_per_pos() (Alignment method) (ArrayAlignment method) probs_per_seq() (Alignment method) (ArrayAlignment method) (SequenceCollection method) protein (DnaSequence attribute) (RnaSequence attribute) ProteinSequence (class in cogent3.core.sequence) prune() (PhyloNode method) Q quick_tree() (Alignment method) (ArrayAlignment method) R rc() (Alignment method) (ArrayAlignment method) (DnaSequence method) (MolType method) (ProteinSequence 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) (ArrayAlignment method) (SequenceCollection method) replace() (DnaSequence method) (ProteinSequence method) (RnaSequence method) replace_annotation_db() (DnaSequence method) (ProteinSequence method) (RnaSequence method) replace_seqs() (Alignment method) (ArrayAlignment method) resolve_ambiguity() (MolType method) resolved_ambiguities() (DnaSequence method) (ProteinSequence method) (RnaSequence method) reverse_complement() (Alignment method) (ArrayAlignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) reversed (Feature property) RnaSequence (class in cogent3.core.sequence) root() (PhyloNode method) root_at_midpoint() (PhyloNode method) rooted_at() (PhyloNode method) rooted_with_tip() (PhyloNode method) S same_shape() (PhyloNode method) same_topology() (PhyloNode method) sample() (Alignment method) (ArrayAlignment method) scale_branch_lengths() (PhyloNode method) separation() (PhyloNode method) seqid (Feature property) seqlogo() (Alignment method) (ArrayAlignment method) seqs (Alignment property) (ArrayAlignment property) (SequenceCollection property) SequenceCollection (class in cogent3.core.alignment) set_max_tip_tip_distance() (PhyloNode method) set_param_value() (PhyloNode method) set_repr_policy() (Alignment method) (ArrayAlignment 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) sliding_windows() (Alignment method) (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) sorted() (PhyloNode method) (Table method) source (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) space (Table property) store_suffix (DataStoreSqlite attribute) strand_symmetric_motifs() (MolType method) strand_symmetry() (Alignment method) (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) strip_bad() (DnaSequence method) (ProteinSequence method) (RnaSequence method) strip_bad_and_gaps() (DnaSequence method) (ProteinSequence method) (RnaSequence method) strip_degenerate() (DnaSequence 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) T Table (class in cogent3.util.table) table_names (BasicAnnotationDb property) (GenbankAnnotationDb property) (GffAnnotationDb property) tail() (Table method) take_columns() (Columns method) take_positions() (Alignment method) (ArrayAlignment method) take_positions_if() (Alignment method) (ArrayAlignment method) take_seqs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) take_seqs_if() (Alignment method) (ArrayAlignment method) (SequenceCollection method) tip_children() (PhyloNode method) tip_to_tip_distances() (PhyloNode method) tips() (PhyloNode method) tips_within_distance() (PhyloNode method) title (Table property) to_categorical() (Table method) to_csv() (Table method) to_dict() (Alignment method) (ArrayAlignment method) (Columns method) (Feature method) (SequenceCollection method) (Table method) to_dna() (Alignment method) (ArrayAlignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) to_fasta() (Alignment method) (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) to_html() (Alignment method) (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) (Table method) to_indices() (Alphabet method) to_json() (Alignment method) (Alphabet method) (ArrayAlignment method) (BasicAnnotationDb method) (DnaSequence method) (GenbankAnnotationDb method) (GffAnnotationDb method) (MolType method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) (Table method) to_latex() (Table method) to_list() (Table method) to_markdown() (Table method) to_moltype() (Alignment method) (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) to_nexus() (Alignment method) (ArrayAlignment method) (SequenceCollection method) to_pandas() (Table method) to_phylip() (Alignment method) (ArrayAlignment method) (SequenceCollection method) to_plotly() (Table method) to_pretty() (Alignment method) (ArrayAlignment method) to_protein() (Alignment method) (ArrayAlignment method) (SequenceCollection method) to_regex() (GeneticCode method) (MolType method) to_rich_dict() (Alignment method) (Alphabet method) (ArrayAlignment method) (BasicAnnotationDb method) (Columns method) (DnaSequence method) (GenbankAnnotationDb method) (GffAnnotationDb method) (MolType method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) (Table method) to_rna() (Alignment method) (ArrayAlignment 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) (ArrayAlignment 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) (ArrayAlignment 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 valid_on_alphabet() (MolType method) validate() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) values() (Columns method) variable_positions() (Alignment method) (ArrayAlignment method) verify_sequence() (MolType method) W what_ambiguity() (MolType method) with_gap_motif() (Alphabet method) with_gaps_from() (Alignment method) with_masked_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) with_modified_termini() (Alignment method) (ArrayAlignment method) (SequenceCollection method) with_new_column() (Table method) with_new_header() (Table method) with_termini_unknown() (DnaSequence method) (ProteinSequence method) (RnaSequence method) with_traceback() (Alphabet.AlphabetError method) without_lost_spans() (Feature method) write() (Alignment method) (ArrayAlignment 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)
