Index

A

adapt_motif_probs() (Alphabet method) add_annotation() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) add_column_from_str() (Columns method) add_feature() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) add_from_ref_aln() (Alignment method) (ArrayAlignment method) add_note() (Alphabet.AlphabetError 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) annotations (Alignment attribute) (DnaSequence attribute) (ProteinSequence attribute) (RnaSequence attribute) 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) ascii_art() (PhyloNode method) attach_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence 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)

bifurcating() (PhyloNode 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) clear() (Columns method) clear_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) codon_alphabet() (DnaSequence method) (RnaSequence method) coevolution() (Alignment method) (ArrayAlignment method) cogent.app cogent.db.ensembl cogent.db.eutils cogent.maths.unifrac cogent.motif cogent.seqsim cogent.struct 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) complement() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method)

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_recursive() (PhyloNode 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_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) (Alphabet 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

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) detach_annotations() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method)

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) distinct_values() (Table method) DnaSequence (class in cogent3.core.sequence) dotplot() (Alignment method) (ArrayAlignment method) (SequenceCollection method)

E

entropy_per_pos() (Alignment method) (ArrayAlignment method) entropy_per_seq() (Alignment method) (ArrayAlignment method) (SequenceCollection method)

extend() (PhyloNode method)

F

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_indices() (Alphabet method) from_ordinals_to_seq() (Alphabet method) from_seq_to_array() (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) GeneticCode (class in cogent3.core.genetic_code) get() (Columns method) get_ambiguous_positions() (Alignment method) (ArrayAlignment method) (SequenceCollection method) get_annotations_from_any_seq() (Alignment method) get_annotations_from_seq() (Alignment method) get_annotations_matching() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_by_annotation() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence method) get_by_seq_annotation() (Alignment method) get_code() (in module cogent3.__init__) get_columns() (Table method) get_connecting_edges() (PhyloNode method) get_connecting_node() (PhyloNode 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) (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_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_matched_array() (Alphabet 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_newick_recursive() (PhyloNode method) get_node_matching_name() (PhyloNode method) get_node_names() (PhyloNode method) get_nodes_dict() (PhyloNode method) get_orf_positions() (DnaSequence method) (RnaSequence method) get_param_value() (PhyloNode method) get_position_indices() (Alignment method) (ArrayAlignment method) get_projected_annotations() (Alignment method) get_region_covering_all() (Alignment method) (DnaSequence method) (ProteinSequence method) (RnaSequence 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_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) gettype() (DnaSequence method) (MolType method) (ProteinSequence method) (RnaSequence method)

H

has_terminal_stop() (DnaSequence method) (RnaSequence method) has_terminal_stops() (Alignment method) (ArrayAlignment 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_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) line_wrap (DnaSequence attribute) (ProteinSequence attribute) (RnaSequence attribute)

load_aligned_seqs() (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__) 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_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__) matching_ref() (Alignment method) (ArrayAlignment method) matrix_distance() (DnaSequence method) (ProteinSequence method) (RnaSequence method) max_tip_tip_distance() (PhyloNode method) moltype (Alignment attribute) (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_unnamed_nodes() (PhyloNode method) named_seqs (ArrayAlignment property) no_degenerates() (Alignment method) (ArrayAlignment method) non_tip_children() (PhyloNode method)

nontips() (PhyloNode method) normalized() (Table 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) order (Columns property)

P

pad_seqs() (Alignment method) (ArrayAlignment method) (SequenceCollection method) pairs (Alphabet property) parent (PhyloNode property) 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) project_annotation() (Alignment method) PROTEIN (DnaSequence attribute) protein (DnaSequence attribute) PROTEIN (RnaSequence attribute) protein (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) reassign_names() (PhyloNode 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_seqs() (Alignment method) (ArrayAlignment method)

resolve_ambiguity() (Alphabet method) resolveambiguities() (DnaSequence method) (ProteinSequence method) (RnaSequence method) resolved_ambiguities() (DnaSequence method) (ProteinSequence method) (RnaSequence method) reverse_complement() (Alignment method) (ArrayAlignment method) (DnaSequence method) (RnaSequence method) (SequenceCollection method) 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) 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) 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) space (Table property) 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) subset() (PhyloNode method) subsets() (PhyloNode method) sum_columns() (Table method) sum_rows() (Table method) summed() (Table method)

T

Table (class in cogent3.util.table) 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_dataframe() (Table method) to_dict() (Alignment method) (ArrayAlignment method) (Columns 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) (Table method) to_indices() (Alphabet method) to_json() (Alignment method) (Alphabet method) (ArrayAlignment method) (DnaSequence method) (MolType method) (PhyloNode method) (ProteinSequence method) (RnaSequence method) (SequenceCollection method) (Table method) to_latex() (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_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) (Columns method) (DnaSequence 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) tolist() (Table method) total_descending_branch_length() (PhyloNode method) total_length() (PhyloNode method) translate() (DnaSequence method) (GeneticCode method) (ProteinSequence method) (RnaSequence method) transposed() (Table method) traverse() (PhyloNode method) traverse_recursive() (PhyloNode method) trim_stop_codon() (DnaSequence method) (RnaSequence method) trim_stop_codons() (Alignment method) (ArrayAlignment method) (SequenceCollection method) Triples (Alphabet property)

U

unrooted() (PhyloNode method)

unrooted_deepcopy() (PhyloNode method) update() (Columns method)

V

valid_on_alphabet() (MolType 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) write() (Alignment method) (ArrayAlignment method) (PhyloNode method) (SequenceCollection method) (Table method)