Index

A

absolute_position() (SliceRecord method) add_column_from_str() (Columns method) add_feature() (Alignment method), [1] (BasicAnnotationDb method) (DnaSequence method), [1] (GenbankAnnotationDb method) (GffAnnotationDb method) (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] add_from_ref_aln() (Alignment method) (ArrayAlignment method) add_note() (Alphabet.AlphabetError method) add_records() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) add_seqs() (AlignedSeqsData method) (Alignment method), [1] (ArrayAlignment method) (SeqsData method) (SequenceCollection method), [1] 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.alignment) (class in cogent3.core.new_alignment) alignment_quality() (Alignment method), [1] (ArrayAlignment method) alphabet (AlignedDataView attribute) (AlignedSeqsData property) (ArrayAlignment attribute) Alphabet (class in cogent3.core.alphabet) alphabet (MolType property) (SeqDataView attribute) (SeqsData property) (SeqView attribute) Alphabet.AlphabetError ambiguities (MolType attribute) ancestors() (PhyloNode method) annotate_from_gff() (Alignment method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method)

annotate_matches_to() (Aligned method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] annotation_db (Aligned property) (Alignment property), [1] (ArrayAlignment property) (DnaSequence property), [1] (ProteinSequence property), [1] (RnaSequence property), [1] (SequenceCollection property), [1] annotation_offset (DnaSequence property), [1] (ProteinSequence property), [1] (RnaSequence property), [1] anticodons (GeneticCode attribute) append() (PhyloNode method) appended() (Table method) apply_pssm() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] apply_scaled_gaps() (Alignment method) args (Alphabet.AlphabetError attribute) 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) ArrayAlignment (class in cogent3.core.alignment) 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)

blocks (GeneticCode property) bytes_value (AlignedDataView property) (SeqDataView property) (SeqView property)

C

can_match() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] can_mismatch() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) can_mispair() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method) (RnaSequence method), [1] can_pair() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method) (RnaSequence method), [1] changes() (GeneticCode 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) codon_alphabet (DnaSequence attribute) (RnaSequence attribute) codons (GeneticCode attribute) coerce_str() (MolType method) coerce_to (MolType attribute) coevolution() (Alignment method), [1] (ArrayAlignment method) cogent.app cogent.db.ensembl cogent.db.eutils cogent.maths.unifrac cogent.motif cogent.seqsim cogent.struct cogent3.util.misc colors (MolType attribute) 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), [1] (MolType method), [1] (ProteinSequence method) (RnaSequence method), [1] complements (MolType attribute) completed (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) completed members convert_seq_array_to() (CharAlphabet method) copy() (AlignedDataView method) (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (PhyloNode method) (ProteinSequence method), [1] (RnaSequence method), [1] (SeqDataView method) (SequenceCollection method) (SeqView method) (SliceRecord method)

copy_annotations() (Alignment method), [1] (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] copy_topology() (PhyloNode method) count() (Alphabet method) (CharAlphabet method) (DnaSequence method), [1] (KmerAlphabet method) (ProteinSequence method), [1] (RnaSequence method), [1] (Table method) count_ambiguous() (DnaSequence method) (ProteinSequence method) (RnaSequence method) count_ambiguous_per_seq() (Alignment method) (SequenceCollection method) count_degenerate() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] count_distinct() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) count_gaps() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] count_gaps_per_pos() (Alignment method), [1] (ArrayAlignment method) count_gaps_per_seq() (Alignment method), [1] (ArrayAlignment method) count_unique() (Table method) count_variants() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) counts() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] counts_per_pos() (Alignment method), [1] (ArrayAlignment method) counts_per_seq() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] 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), [1] (ArrayAlignment method) (PhyloNode method) (SequenceCollection method) default_gap (Alignment attribute) (ArrayAlignment attribute) define_app() (in module cogent3.app.composable) degap() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] degen_alphabet (MolType property) degen_gapped_alphabet (MolType property) degenerate_from_seq() (MolType method), [1] 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), [1] (ProteinSequence method), [1] (RnaSequence method), [1] disambiguate() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] distance() (DnaSequence method), [1] (PhyloNode method) (ProteinSequence method), [1] (RnaSequence method), [1] distance_matrix() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] distinct_values() (Table method) DnaSequence (class in cogent3.core.new_sequence) (class in cogent3.core.sequence) dotplot() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] drop_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method)

E

entropy_per_pos() (Alignment method), [1] (ArrayAlignment method) entropy_per_seq() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1]

extend() (PhyloNode method)

F

Feature (class in cogent3.core.annotation) filtered() (Alignment method), [1] (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), [1] (ProteinSequence method), [1] (RnaSequence method), [1] frac_diff_gaps() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] frac_diff_non_gaps() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1]

frac_same() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] frac_same_gaps() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] frac_same_non_gaps() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] frac_similar() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] from_dict() (BasicAnnotationDb class method) (GenbankAnnotationDb class method) (GffAnnotationDb class method) from_index() (KmerAlphabet method) from_indices() (Alphabet method) (CharAlphabet method) (KmerAlphabet 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) (SequenceCollection class method) from_seqs() (AlignedSeqsData class method) (SeqsData class method) from_seqs_and_gaps() (AlignedSeqsData class method)

G

gap (MolType attribute) gap_char (Alphabet property) (CharAlphabet property) (KmerAlphabet property) gap_chars (Alignment attribute) (ArrayAlignment attribute) gap_index (CharAlphabet property) (KmerAlphabet property) gap_indices() (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] gap_maps() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) gap_vector() (Aligned method) (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] gapped_alphabet (MolType property) gapped_array_value (AlignedDataView property) gapped_by_map() (Alignment method), [1] (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] gapped_by_map_motif_iter() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] gapped_by_map_segment_iter() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] 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.genetic_code) (class in cogent3.core.new_genetic_code) get() (Columns method) get_alphabet() (GeneticCode method), [1] get_ambiguous_positions() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] 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), [1] get_degapped_relative_to() (Alignment method), [1] (ArrayAlignment method) get_degenerate_positions() (MolType method), [1] get_distances() (PhyloNode method) get_drawable() (Alignment method), [1] (DnaSequence method), [1] (Feature method) (ProteinSequence method), [1] (RnaSequence method), [1] get_drawables() (Alignment method), [1] (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] 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), [1] (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] get_features_matching() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_figure() (PhyloNode method) get_gap_array() (Alignment method), [1] (ArrayAlignment method) get_gap_motif() (Alphabet method) get_gapped_seq() (Alignment method), [1] (ArrayAlignment 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), [1] (ArrayAlignment method) (SequenceCollection method), [1] get_in_motif_size() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] get_kmer_alphabet() (CharAlphabet method) get_kmers() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] get_lengths() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] get_max_tip_tip_distance() (PhyloNode method) get_model() (in module cogent3.__init__) get_moltype() (in module cogent3.__init__) get_motif_len() (Alphabet method) (CharAlphabet method) get_motif_probs() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] get_name() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] 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), [1] (ArrayAlignment method) get_positions() (AlignedSeqsData method) get_projected_feature() (Alignment method), [1] get_projected_features() (Alignment method), [1] get_records_matching() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) get_row_indices() (Table method) get_seq() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] get_seq_array() (AlignedSeqsData method) (SeqsData method) get_seq_bytes() (AlignedSeqsData method) (SeqsData method) get_seq_indices() (Alignment method) (ArrayAlignment method) (SequenceCollection 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), [1] (ArrayAlignment method) (SequenceCollection method), [1] get_slice() (Feature method) get_stop_indices() (GeneticCode method) get_sub_alignment() (ArrayAlignment method) get_sub_tree() (PhyloNode method) get_subset() (Alphabet method) (CharAlphabet method) get_tip_names() (PhyloNode method) get_translation() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] get_type() (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] get_ungapped() (AlignedSeqsData method) get_view() (AlignedSeqsData method) (SeqsData method) get_word_alphabet() (Alphabet method) (CharAlphabet method) get_xml() (PhyloNode method) GffAnnotationDb (class in cogent3.core.annotation_db)

H

has_ambiguity() (MolType method) has_terminal_stop() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1]

head() (Table method) header (Table property)

I

ID (GeneticCode attribute) includes_gap_motif() (Alphabet method) index() (Alphabet method) (CharAlphabet method) (KmerAlphabet method) index_in_parent() (PhyloNode method) index_name (Columns property) (Table property) info (DnaSequence attribute) (ProteinSequence attribute) (RnaSequence attribute) information_plot() (Alignment method), [1] (ArrayAlignment method) inner_join() (Table method) insert() (PhyloNode method) is_ambiguity() (MolType method), [1] is_annotated() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] is_array (Alignment attribute) (ArrayAlignment attribute) (SequenceCollection attribute) is_compatible_alphabet() (MolType method), [1] is_degenerate() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] is_gap() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) is_gapped() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] is_nucleic (MolType property), [1] is_ragged() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1]

is_reversed (AlignedDataView property) (SeqDataView property) (SeqView property) (SliceRecord property) is_root() (PhyloNode method) is_start() (GeneticCode method) is_stop() (GeneticCode method), [1] is_strict() (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] is_tip() (PhyloNode method) is_valid() (Alphabet method) (CharAlphabet method) (DnaSequence method), [1] (KmerAlphabet method) (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] isroot() (PhyloNode method) istip() (PhyloNode method) items() (Columns method) iter_alphabets() (MolType method) iter_kmers() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] iter_nontips() (PhyloNode method) iter_positions() (Alignment method), [1] (ArrayAlignment method) iter_rows() (Columns method) iter_selected() (Alignment method) (ArrayAlignment method) (SequenceCollection method) iter_seqs() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] iter_tips() (PhyloNode method) iupac_consensus() (Alignment method), [1] (ArrayAlignment 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) 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), [1] (ArrayAlignment method) make_aligned_seqs() (in module cogent3.__init__) make_array_seq() (MolType method), [1] make_feature() (Aligned method) (Alignment method), [1] (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] make_indexes() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) make_seq() (in module cogent3.__init__) (MolType method), [1] 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), [1] (ArrayAlignment method) matching_rules (MolType property) matrix_distance() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] 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)

missing_index (CharAlphabet property) (KmerAlphabet property) mode (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) moltype (Aligned property) (Alignment attribute) (Alphabet property) (ArrayAlignment attribute) (CharAlphabet property) MolType (class in cogent3.core.moltype) (class in cogent3.core.new_moltype) moltype (DnaSequence attribute), [1] (GeneticCode attribute) (KmerAlphabet property) (ProteinSequence attribute), [1] (RnaSequence attribute), [1] (SequenceCollection attribute) monomers (MolType attribute) most_degen_alphabet() (MolType method) motif_len (Alphabet property) (CharAlphabet property) (KmerAlphabet property) multifurcating() (PhyloNode method) must_match() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method) must_pair() (DnaSequence method), [1] (MolType method) (ProteinSequence method) (RnaSequence method), [1] mw() (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] mw_calculator (MolType attribute)

N

name (Aligned property) (DnaSequence attribute) (Feature property) (GeneticCode attribute) (MolType attribute) (ProteinSequence attribute) (RnaSequence attribute) name_unnamed_nodes() (PhyloNode method) named_seqs (Alignment property), [1] (ArrayAlignment property) (SequenceCollection property), [1] names (AlignedSeqsData property) (Alignment property) (SeqsData property) (SequenceCollection property) ncbi_code_sequence (GeneticCode attribute)

ncbi_start_codon_map (GeneticCode attribute) no_degenerates() (Alignment method), [1] (ArrayAlignment 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) num_matches() (BasicAnnotationDb method) (GenbankAnnotationDb method) (GffAnnotationDb method) num_seqs (Alignment property), [1] (ArrayAlignment property) (SequenceCollection property), [1]

O

offset (AlignedDataView property) (AlignedSeqsData property) (SeqDataView property) (SeqsData property) (SeqView property) (SliceRecord property) omit_bad_seqs() (Alignment method), [1] (ArrayAlignment method) omit_gap_pos() (Alignment method), [1] (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), [1] (ArrayAlignment method) (SequenceCollection method), [1] pairing_rules (MolType attribute) parent (AlignedDataView attribute) (Feature property) (PhyloNode property) (SeqDataView attribute) (SeqView attribute) parent_coordinates() (Aligned method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] 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), [1] (ProteinSequence method), [1] (RnaSequence method), [1] 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), [1] (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), [1] (ArrayAlignment method) probs_per_seq() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] protein (DnaSequence attribute) (RnaSequence attribute) ProteinSequence (class in cogent3.core.new_sequence) (class in cogent3.core.sequence) prune() (PhyloNode method)

Q

quick_tree() (Alignment method), [1] (ArrayAlignment method)

R

random_disambiguate() (MolType method) rc() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (MolType method), [1] (ProteinSequence method) (RnaSequence method), [1] (SequenceCollection method), [1] 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), [1] (ArrayAlignment method) (SequenceCollection method), [1]

replace() (DnaSequence method) (ProteinSequence method) (RnaSequence method) replace_annotation_db() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] replace_seqs() (Alignment method) (ArrayAlignment method) resolve_ambiguity() (MolType method), [1] resolved_ambiguities() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] reverse_complement() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] reversed (Feature property) RnaSequence (class in cogent3.core.new_sequence) (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), [1] (ArrayAlignment method) scale_branch_lengths() (PhyloNode method) sense_codons (GeneticCode property) 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), [1] (ArrayAlignment method) seqs (Alignment property), [1] (ArrayAlignment property) (SequenceCollection property), [1] SeqsData (class in cogent3.core.new_alignment) SequenceCollection (class in cogent3.core.alignment) (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), [1] (ArrayAlignment method) (SequenceCollection method), [1] (Table method) set_tip_distances() (PhyloNode method) setdefault() (Columns method) shadow() (Feature method) shape (Table property) shuffle() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] siblings() (PhyloNode method) sixframes() (GeneticCode method), [1] slice_record (AlignedDataView property) (SeqDataView property) (SeqView property) slice_with_map() (Aligned method) SliceRecord (class in cogent3.core.new_sequence) sliding_windows() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] sorted() (PhyloNode method) (Table method)

source (DataStoreDirectory property) (DataStoreSqlite property) (ReadOnlyDataStoreZipped property) space (Table property) start (SliceRecord attribute) start_codons (GeneticCode property) step (SliceRecord attribute) stop (SliceRecord attribute) stop_codons (GeneticCode property) store_suffix (DataStoreSqlite attribute) str_value (AlignedDataView property) (SeqDataView property) (SeqView property) strand_symmetric_motifs() (MolType method), [1] strand_symmetry() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (ProteinSequence method) (RnaSequence method), [1] (SequenceCollection method), [1] strip_bad() (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] strip_bad_and_gaps() (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] strip_degenerate() (DnaSequence method), [1] (MolType method) (ProteinSequence method), [1] (RnaSequence method), [1] 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.util.table) table_names (BasicAnnotationDb property) (GenbankAnnotationDb property) (GffAnnotationDb property) tail() (Table method) take_columns() (Columns method) take_positions() (Alignment method), [1] (ArrayAlignment method) take_positions_if() (Alignment method), [1] (ArrayAlignment method) take_seqs() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] take_seqs_if() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1] tip_children() (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), [1] (ArrayAlignment method) (Columns method) (Feature method) (SequenceCollection method), [1] (Table method) to_dna() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] to_fasta() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] to_html() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] (Table method) to_index() (KmerAlphabet method) to_indices() (Alphabet method) (CharAlphabet method) (KmerAlphabet method) to_json() (Alignment method), [1] (Alphabet method) (ArrayAlignment method) (BasicAnnotationDb method) (CharAlphabet method) (DnaSequence method), [1] (GenbankAnnotationDb method) (GffAnnotationDb method) (KmerAlphabet method) (MolType method), [1] (PhyloNode method) (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] (Table method)

to_latex() (Table method) to_list() (Table method) to_markdown() (Table method) to_moltype() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] to_nexus() (Alignment method) (ArrayAlignment method) (SequenceCollection method) to_pandas() (Table method) to_phylip() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method), [1] to_plotly() (Table method) to_pretty() (Alignment method), [1] (ArrayAlignment method) to_protein() (Alignment method) (ArrayAlignment method) (SequenceCollection method) to_regex() (GeneticCode method), [1] (MolType method), [1] to_rich_dict() (Alignment method), [1] (Alphabet method) (ArrayAlignment method) (BasicAnnotationDb method) (CharAlphabet method) (Columns method) (DnaSequence method), [1] (GenbankAnnotationDb method) (GffAnnotationDb method) (KmerAlphabet method) (MolType method), [1] (PhyloNode method) (ProteinSequence method), [1] (RnaSequence method), [1] (SeqDataView method) (SequenceCollection method), [1] (SliceRecord method) (Table method) to_rna() (Alignment method), [1] (ArrayAlignment method) (DnaSequence method), [1] (RnaSequence method), [1] (SequenceCollection method), [1] to_rst() (Table method) to_string() (Table method) to_table() (GeneticCode method), [1] to_tsv() (Table method) to_type() (Alignment method), [1] (ArrayAlignment method) total_descending_branch_length() (PhyloNode method) total_length() (PhyloNode method) translate() (GeneticCode method), [1] transposed() (Table method) traverse() (PhyloNode method) tree_distance() (PhyloNode method) trim_stop_codon() (DnaSequence method), [1] (RnaSequence method), [1] trim_stop_codons() (Alignment method), [1] (ArrayAlignment method) (SequenceCollection method), [1]

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), [1] (ArrayAlignment method) verify_sequence() (MolType method)

W

what_ambiguity() (MolType method) with_gap_motif() (Alphabet method) (CharAlphabet method) (KmerAlphabet method) with_gaps_from() (Alignment method) with_masked_annotations() (Alignment method), [1] (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1] with_modified_termini() (Alignment method) (ArrayAlignment method) (SequenceCollection method) with_new_column() (Table method) with_new_header() (Table method) with_offset() (AlignedDataView method) (SeqDataView method) (SeqView method) with_termini_unknown() (DnaSequence method), [1] (ProteinSequence method), [1] (RnaSequence method), [1]

with_traceback() (Alphabet.AlphabetError method) without_lost_spans() (Feature method) write() (Alignment method), [1] (ArrayAlignment method) (BasicAnnotationDb method) (DataStoreDirectory method) (DataStoreSqlite method) (GenbankAnnotationDb method) (GffAnnotationDb method) (PhyloNode method) (ReadOnlyDataStoreZipped method) (SequenceCollection method), [1] (Table method) write_log() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method) write_not_completed() (DataStoreDirectory method) (DataStoreSqlite method) (ReadOnlyDataStoreZipped method)