Index

A

acquire() (dendropy.interop.genbank.GenBankResourceStore method) acquire_range() (dendropy.interop.genbank.GenBankResourceStore method) add() (dendropy.dataobject.dataset.DataSet method) add_bibtex() (dendropy.dataobject.base.AnnotationSet method) add_bound_attribute() (dendropy.dataobject.base.AnnotationSet method) add_char_matrix() (dendropy.dataobject.dataset.DataSet method) add_character_subset() (dendropy.dataobject.char.CharacterMatrix method) add_child() (dendropy.dataobject.tree.Node method) add_citation() (dendropy.dataobject.base.AnnotationSet method) add_new() (dendropy.dataobject.base.AnnotationSet method) add_taxon() (dendropy.dataobject.taxon.TaxonSet method) add_taxon_set() (dendropy.dataobject.dataset.DataSet method) add_tree_list() (dendropy.dataobject.dataset.DataSet method) adjacent_edges (dendropy.dataobject.tree.Edge attribute)

adjacent_nodes() (dendropy.dataobject.tree.Node method) age_order_iter() (dendropy.dataobject.tree.Node method) age_order_node_iter() (dendropy.dataobject.tree.Tree method) all_taxa_bitmask() (dendropy.dataobject.taxon.TaxonSet method) ambiguous_states() (dendropy.dataobject.char.StateAlphabet method) ancestor_iter() (dendropy.dataobject.tree.Node method) Annotation (class in dendropy.dataobject.base) AnnotationSet (class in dendropy.dataobject.base) append() (dendropy.dataobject.tree.TreeList method) as_ascii_plot() (dendropy.dataobject.tree.Tree method) as_newick_string() (dendropy.dataobject.tree.Node method) (dendropy.dataobject.tree.Tree method) as_python_source() (dendropy.dataobject.tree.Tree method) (dendropy.dataobject.tree.TreeList method) attach_taxon_set() (dendropy.dataobject.dataset.DataSet method)

B

birth_death() (in module dendropy.treesim) bounce_constrain() (in module dendropy.continuous) brlen_dists_calc() (in module dendropy.treecalc)

brlen_scores_calc() (in module dendropy.treecalc) build_edge_taxa_sets() (dendropy.reconcile.ContainingTree method)

C

calc() (dendropy.treecalc.PatristicDistanceMatrix method) calc_node_ages() (dendropy.dataobject.tree.Tree method) char (module) CharacterDataCell (class in dendropy.dataobject.char) CharacterDataMap (class in dendropy.dataobject.char) CharacterDataVector (class in dendropy.dataobject.char) CharacterMatrix (class in dendropy.dataobject.char) CharacterSubset (class in dendropy.dataobject.char) CharacterType (class in dendropy.dataobject.char) child_nodes() (dendropy.dataobject.tree.Node method) clear() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.taxon.TaxonSet method) (dendropy.reconcile.ContainingTree method) clear_contained_edges() (dendropy.reconcile.ContainingTree method) clone_from() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.tree.Tree method) cmp() (dendropy.dataobject.taxon.Taxon static method) coalesce() (in module dendropy.coalescent) coalescence_intervals() (dendropy.dataobject.tree.Tree method) coalescent (module)

collapse() (dendropy.dataobject.tree.Edge method) collapse_clade() (dendropy.dataobject.tree.Node method) (in module dendropy.treemanip) collapse_conflicting() (in module dendropy.treemanip) collapse_edge() (in module dendropy.treemanip) collapse_unweighted_edges() (dendropy.dataobject.tree.Tree method) complement_split_bitmask() (dendropy.dataobject.taxon.TaxonSet method) concatenate() (dendropy.dataobject.char.CharacterMatrix class method) concatenate_from_paths() (dendropy.dataobject.char.CharacterMatrix class method) concatenate_from_streams() (dendropy.dataobject.char.CharacterMatrix class method) consensus() (dendropy.dataobject.tree.TreeList method) constrained_kingman() (in module dendropy.treesim) contained_coalescent() (in module dendropy.treesim) ContainingTree (class in dendropy.reconcile) continuous (module) ContinuousCharacterMatrix (class in dendropy.dataobject.char) contrasts_tree() (dendropy.continuous.PhylogeneticIndependentConstrasts method) create_taxon_to_state_set_map() (dendropy.dataobject.char.CharacterMatrix method)

D

DataObject (class in dendropy.dataobject.base) DataSet (class in dendropy.dataobject.dataset) dataset (module) deep_coalescences() (dendropy.reconcile.ContainingTree method) default_oid (dendropy.dataobject.base.DataObject attribute) dendropy.coalescent (module) dendropy.continuous (module) dendropy.dataobject.base (module) dendropy.dataobject.char (module) dendropy.dataobject.taxa (module) dendropy.dataobject.tree (module) dendropy.reconcile (module) dendropy.treecalc (module)

dendropy.treemanip (module) dendropy.treesim (module) deroot() (dendropy.dataobject.tree.Tree method) description() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.dataset.DataSet method) (dendropy.dataobject.taxon.Taxon method) (dendropy.dataobject.taxon.TaxonSet method) (dendropy.dataobject.tree.Edge method) (dendropy.dataobject.tree.Node method) (dendropy.dataobject.tree.Tree method) (dendropy.dataobject.tree.TreeList method) discrete_birth_death() (in module dendropy.treesim) discrete_time_to_coalescence() (in module dendropy.coalescent) DiscreteCharacterMatrix (class in dendropy.dataobject.char) distance_from_root() (dendropy.dataobject.tree.Node method) distance_from_tip() (dendropy.dataobject.tree.Node method) distances() (dendropy.treecalc.PatristicDistanceMatrix method) DnaCharacterMatrix (class in dendropy.dataobject.char) drop() (dendropy.dataobject.base.AnnotationSet method)

E

Edge (class in dendropy.dataobject.tree) edge (dendropy.dataobject.tree.Node attribute) edge_length (dendropy.dataobject.tree.Node attribute) embed_contained_kingman() (dendropy.reconcile.ContainingTree method) embed_tree() (dendropy.reconcile.ContainingTree method) euclidean_distance() (dendropy.dataobject.tree.Tree method) (in module dendropy.treecalc) expected_tmrca() (in module dendropy.coalescent)

export_character_indices() (dendropy.dataobject.char.CharacterMatrix method) export_character_subset() (dendropy.dataobject.char.CharacterMatrix method) extend() (dendropy.dataobject.char.CharacterDataMap method) (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.char.StandardCharacterMatrix method) (dendropy.dataobject.tree.TreeList method) extend_characters() (dendropy.dataobject.char.CharacterDataMap method) (dendropy.dataobject.char.CharacterMatrix method) extend_map() (dendropy.dataobject.char.CharacterMatrix method) extract_coalescent_frames() (in module dendropy.coalescent)

F

false_positives_and_negatives() (dendropy.dataobject.tree.Tree method) (in module dendropy.treecalc) find() (dendropy.dataobject.base.AnnotationSet method) find_edge() (dendropy.dataobject.tree.Tree method) find_missing_splits() (dendropy.dataobject.tree.Tree method) find_node() (dendropy.dataobject.tree.Tree method) find_node_with_label() (dendropy.dataobject.tree.Tree method) find_node_with_taxon() (dendropy.dataobject.tree.Tree method) find_node_with_taxon_label() (dendropy.dataobject.tree.Tree method) findall() (dendropy.dataobject.base.AnnotationSet method) fit_edge_lengths() (dendropy.reconcile.ContainingTree method)

fitch_down_pass() (in module dendropy.treecalc) fitch_up_pass() (in module dendropy.treecalc) FixedStateAlphabetElement (class in dendropy.dataobject.char) frequency_of_split() (dendropy.dataobject.tree.TreeList method) fundamental_ids (dendropy.dataobject.char.StateAlphabetElement attribute) fundamental_states (dendropy.dataobject.char.StateAlphabetElement attribute) fundamental_states() (dendropy.dataobject.char.StateAlphabet method) fundamental_symbols (dendropy.dataobject.char.StateAlphabetElement attribute) fundamental_tokens (dendropy.dataobject.char.StateAlphabetElement attribute)

G

genbank (module) GenBankAccessionFeature (class in dendropy.interop.genbank) GenBankAccessionFeatures (class in dendropy.interop.genbank) GenBankAccessionInterval (class in dendropy.interop.genbank) GenBankAccessionOtherSeqIds (class in dendropy.interop.genbank) GenBankAccessionQualifier (class in dendropy.interop.genbank) GenBankAccessionQualifiers (class in dendropy.interop.genbank) GenBankAccessionRecord (class in dendropy.interop.genbank) GenBankAccessionReference (class in dendropy.interop.genbank) GenBankAccessionReferences (class in dendropy.interop.genbank) GenBankDna (class in dendropy.interop.genbank) GenBankProtein (class in dendropy.interop.genbank) GenBankResourceStore (class in dendropy.interop.genbank) GenBankRna (class in dendropy.interop.genbank) generate_char_matrix() (dendropy.interop.genbank.GenBankResourceStore method) get() (dendropy.dataobject.char.CharacterMatrix method) get_adjacent_edges() (dendropy.dataobject.tree.Edge method)

get_adjacent_nodes() (dendropy.dataobject.tree.Node method) get_default_taxon_set() (dendropy.dataobject.dataset.DataSet method) get_edge_set() (dendropy.dataobject.tree.Tree method) get_incident_edges() (dendropy.dataobject.tree.Node method) get_length_diffs() (in module dendropy.treecalc) get_node_set() (dendropy.dataobject.tree.Tree method) get_node_str() (dendropy.dataobject.tree.Node method) get_state() (dendropy.dataobject.char.StateAlphabet method) get_states() (dendropy.dataobject.char.StateAlphabet method) get_states_as_cells() (dendropy.dataobject.char.StateAlphabet method) get_states_as_vector() (dendropy.dataobject.char.StateAlphabet method) get_taxa() (dendropy.dataobject.taxon.TaxonSet method) get_taxa_bitmask() (dendropy.dataobject.taxon.TaxonSet method) get_taxon() (dendropy.dataobject.taxon.TaxonSet method) get_tree_list() (dendropy.dataobject.dataset.DataSet method) get_value() (dendropy.dataobject.base.AnnotationSet method)

H

has_key() (dendropy.dataobject.char.CharacterMatrix method) has_taxa() (dendropy.dataobject.taxon.TaxonSet method)

has_taxon() (dendropy.dataobject.taxon.TaxonSet method)

I

id_chartype_map() (dendropy.dataobject.char.CharacterMatrix method) id_state_map() (dendropy.dataobject.char.StateAlphabet method) incident_edges() (dendropy.dataobject.tree.Node method) infer_taxa() (dendropy.dataobject.tree.Tree method) InfiniteSitesCharacterMatrix (class in dendropy.dataobject.char) internal_nodes() (dendropy.dataobject.tree.Tree method) is_exact_correspondence() (dendropy.dataobject.char.StateAlphabetElement method) is_gap_state() (dendropy.dataobject.char.StateAlphabet method)

is_internal() (dendropy.dataobject.tree.Edge method) (dendropy.dataobject.tree.Node method) is_leaf() (dendropy.dataobject.tree.Node method) is_terminal() (dendropy.dataobject.tree.Edge method) items() (dendropy.dataobject.char.CharacterMatrix method) iteritems() (dendropy.dataobject.char.CharacterMatrix method) iterkeys() (dendropy.dataobject.char.CharacterMatrix method) itervalues() (dendropy.dataobject.char.CharacterMatrix method)

K

keys() (dendropy.dataobject.char.CharacterMatrix method) kl_divergence_coalescent_trees() (in module dendropy.coalescent)

kl_divergence_coalescent_waiting_times() (in module dendropy.coalescent)

L

labels() (dendropy.dataobject.taxon.TaxonSet method) ladderize() (dendropy.dataobject.tree.Tree method) leaf_edge_iter() (dendropy.dataobject.tree.Tree method) leaf_iter() (dendropy.dataobject.tree.Node method) (dendropy.dataobject.tree.Tree method) leaf_nodes() (dendropy.dataobject.tree.Node method) (dendropy.dataobject.tree.Tree method) length() (dendropy.dataobject.tree.Tree method)

level() (dendropy.dataobject.tree.Node method) level_order_edge_iter() (dendropy.dataobject.tree.Tree method) level_order_iter() (dendropy.dataobject.tree.Node method) level_order_node_iter() (dendropy.dataobject.tree.Tree method) log_probability_of_coalescent_frames() (in module dendropy.coalescent) log_probability_of_coalescent_tree() (in module dendropy.coalescent)

M

mason_gamer_kellogg_score() (in module dendropy.treecalc) match_state() (dendropy.dataobject.char.StateAlphabet method) mean_kingman() (in module dendropy.treesim)

monophyletic_partition_discordance() (in module dendropy.reconcile) mrca() (dendropy.dataobject.tree.Tree method) (dendropy.treecalc.PatristicDistanceMatrix method) multi_states() (dendropy.dataobject.char.StateAlphabet method)

N

new_char_matrix() (dendropy.dataobject.dataset.DataSet method) new_character_subset() (dendropy.dataobject.char.CharacterMatrix method) new_child() (dendropy.dataobject.tree.Node method) new_edge() (dendropy.dataobject.tree.Edge method) new_taxon() (dendropy.dataobject.taxon.TaxonSet method) new_taxon_set() (dendropy.dataobject.dataset.DataSet method) new_tree_list() (dendropy.dataobject.dataset.DataSet method)

Node (class in dendropy.dataobject.tree) node_ages() (dendropy.dataobject.tree.Tree method) node_waiting_time_pairs() (in module dendropy.coalescent) nodes() (dendropy.dataobject.tree.Tree method) nodeset_hash() (dendropy.dataobject.tree.Node static method) NucleotideCharacterMatrix (class in dendropy.dataobject.char) num_deep_coalescences() (dendropy.reconcile.ContainingTree method)

O

oid (dendropy.dataobject.base.DataObject attribute)

P

parent_node (dendropy.dataobject.tree.Node attribute) partition() (dendropy.dataobject.taxon.TaxonSet method) patristic_distance() (in module dendropy.treecalc) PatristicDistanceMatrix (class in dendropy.treecalc) PhylogeneticIndependentConstrasts (class in dendropy.continuous) polymorphic_states() (dendropy.dataobject.char.StateAlphabet method) pop() (dendropy.dataobject.char.CharacterMatrix method) pop_gen_tree() (in module dendropy.treesim) popitem() (dendropy.dataobject.char.CharacterMatrix method) postorder_edge_iter() (dendropy.dataobject.tree.Tree method) postorder_internal_node_iter() (dendropy.dataobject.tree.Node method) (dendropy.dataobject.tree.Tree method) postorder_iter() (dendropy.dataobject.tree.Node method) postorder_node_iter() (dendropy.dataobject.tree.Tree method)

preorder_edge_iter() (dendropy.dataobject.tree.Tree method) preorder_internal_node_iter() (dendropy.dataobject.tree.Node method) (dendropy.dataobject.tree.Tree method) preorder_iter() (dendropy.dataobject.tree.Node method) preorder_node_iter() (dendropy.dataobject.tree.Tree method) print_newick() (dendropy.dataobject.tree.Tree method) print_plot() (dendropy.dataobject.tree.Tree method) ProteinCharacterMatrix (class in dendropy.dataobject.char) prune_leaves_without_taxa() (dendropy.dataobject.tree.Tree method) (in module dendropy.treemanip) prune_subtree() (dendropy.dataobject.tree.Tree method) prune_taxa() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.tree.Tree method) (in module dendropy.treemanip) prune_taxa_with_labels() (dendropy.dataobject.tree.Tree method) pure_kingman() (in module dendropy.treesim) pybus_harvey_gamma() (dendropy.dataobject.tree.Tree method)

R

randomly_assign_taxa() (dendropy.dataobject.tree.Tree method) randomly_reorient_tree() (dendropy.dataobject.tree.Tree method) (in module dendropy.treemanip) randomly_rotate() (dendropy.dataobject.tree.Tree method) (in module dendropy.treemanip) read() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.dataset.DataSet method) (dendropy.dataobject.tree.Tree method) (dendropy.dataobject.tree.TreeList method) rebuild() (dendropy.reconcile.ContainingTree method) reconcile (module) reconciliation_discordance() (in module dendropy.reconcile) reindex_subcomponent_taxa() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.tree.Tree method) (dendropy.dataobject.tree.TreeList method) reindex_tree_taxa() (dendropy.dataobject.tree.TreeList method) reinsert_nodes() (dendropy.dataobject.tree.Node method) remap_to_default_state_alphabet_by_symbol() (dendropy.dataobject.char.DiscreteCharacterMatrix method) remap_to_state_alphabet_by_symbol() (dendropy.dataobject.char.DiscreteCharacterMatrix method) remove_child() (dendropy.dataobject.tree.Node method)

require_taxon() (dendropy.dataobject.taxon.TaxonSet method) reroot_at_edge() (dendropy.dataobject.tree.Tree method) reroot_at_midpoint() (dendropy.dataobject.tree.Tree method) reroot_at_node() (dendropy.dataobject.tree.Tree method) reseed_at() (dendropy.dataobject.tree.Tree method) resolve_polytomies() (dendropy.dataobject.tree.Tree method) RestrictionSitesCharacterMatrix (class in dendropy.dataobject.char) retain_taxa() (dendropy.dataobject.tree.Tree method) (in module dendropy.treemanip) retain_taxa_with_labels() (dendropy.dataobject.tree.Tree method) reversible_remove_child() (dendropy.dataobject.tree.Node method) RnaCharacterMatrix (class in dendropy.dataobject.char) robinson_foulds_calc() (in module dendropy.treecalc) robinson_foulds_distance() (dendropy.dataobject.tree.Tree method) (in module dendropy.treecalc)

S

scale_edges() (dendropy.dataobject.tree.Tree method) set_cell_by_index() (dendropy.dataobject.char.CharacterDataVector method) set_child_nodes() (dendropy.dataobject.tree.Node method) set_children() (dendropy.dataobject.tree.Node method) set_edge_lengths_from_node_ages() (dendropy.dataobject.tree.Tree method) setdefault() (dendropy.dataobject.char.CharacterMatrix method) simulate_contained_kingman() (dendropy.reconcile.ContainingTree method) simulate_continuous() (in module dendropy.continuous) sister_nodes() (dendropy.dataobject.tree.Node method) SitePatterns (class in dendropy.dataobject.char) split_as_newick_string() (dendropy.dataobject.taxon.TaxonSet method) split_bitmask_string() (dendropy.dataobject.taxon.TaxonSet method)

split_taxa_list() (dendropy.dataobject.taxon.TaxonSet method) splits_distance() (in module dendropy.treecalc) StandardCharacterMatrix (class in dendropy.dataobject.char) star_tree() (in module dendropy.treesim) state_for_symbol() (dendropy.dataobject.char.StateAlphabet method) state_index_for_symbol() (dendropy.dataobject.char.StateAlphabet method) StateAlphabet (class in dendropy.dataobject.char) StateAlphabetElement (class in dendropy.dataobject.char) strip_comments() (dendropy.dataobject.tree.Tree method) sum_of_distances() (dendropy.treecalc.PatristicDistanceMatrix method) symbol_state_map() (dendropy.dataobject.char.StateAlphabet method) symmetric_difference() (dendropy.dataobject.tree.Tree method) (in module dendropy.treecalc)

T

Taxon (class in dendropy.dataobject.taxon) taxon_bitmask() (dendropy.dataobject.taxon.TaxonSet method) TaxonSet (class in dendropy.dataobject.taxon) time_to_coalescence() (in module dendropy.coalescent) to_outgroup_position() (dendropy.dataobject.tree.Tree method) Tree (class in dendropy.dataobject.tree)

tree (dendropy.continuous.PhylogeneticIndependentConstrasts attribute) treecalc (module) TreeList (class in dendropy.dataobject.tree) treemanip (module) treesim (module) TreeSimTotalExtinctionException

U

unassign_taxa() (dendropy.dataobject.tree.Tree method) uniform_pure_birth() (in module dendropy.treesim) unify_taxa() (dendropy.dataobject.dataset.DataSet method)

update_allele_waiting_time_dist() (in module dendropy.coalescent) update_splits() (dendropy.dataobject.tree.Tree method) update_taxon_set() (dendropy.dataobject.char.CharacterMatrix method)

V

values() (dendropy.dataobject.char.CharacterMatrix method) values_as_dict() (dendropy.dataobject.base.AnnotationSet method)

vector_size (dendropy.dataobject.char.CharacterDataMap attribute) (dendropy.dataobject.char.CharacterMatrix attribute) vectors() (dendropy.dataobject.char.CharacterMatrix method)

W

write() (dendropy.dataobject.char.CharacterMatrix method) (dendropy.dataobject.dataset.DataSet method) (dendropy.dataobject.tree.Tree method) (dendropy.dataobject.tree.TreeList method) write_as_dot() (dendropy.dataobject.tree.Tree method) write_as_mesquite() (dendropy.reconcile.ContainingTree method)

write_ascii_plot() (dendropy.dataobject.tree.Tree method) write_newick() (dendropy.dataobject.tree.Node method)

X

xprune_taxa() (dendropy.dataobject.tree.Tree method)