Index

_

__init__() (historydag.compact_genome.CompactGenome method) (historydag.dag.EteTreeBuilder method) (historydag.dag.HistoryDag method) (historydag.dag.PreorderHistoryBuilder method) (historydag.dag_node.EdgeSet method) (historydag.dag_node.HistoryDagNode method) (historydag.dag_node.UANode method) (historydag.HistoryDag method), [1] (historydag.HistoryDagNode method), [1] (historydag.parsimony_utils.AmbiguityMap method) (historydag.parsimony_utils.SitewiseTransitionModel method) (historydag.parsimony_utils.TransitionModel method) (historydag.parsimony_utils.UnitTransitionModel method) (historydag.utils.AddFuncDict method) (historydag.utils.DecimalState method) (historydag.utils.FloatState method) (historydag.utils.HistoryDagFilter method) (historydag.utils.IntState method) (historydag.utils.StrState method)

A

access_field() (in module historydag.utils) access_nodefield_default() (in module historydag.utils) add_all_allowed_edges() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) add_edge() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) add_label_fields() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) add_node() (historydag.dag.PreorderTreeBuilder method) add_node_at_all_possible_places() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

add_to_edgeset() (historydag.dag_node.EdgeSet method) AddFuncDict (class in historydag.utils) adjusted_node_probabilities() (historydag.mutation_annotated_dag.CGHistoryDag method) AmbiguityMap (class in historydag.parsimony_utils) ambiguous_cg_diff() (in module historydag.compact_genome) AmbiguousLeafCGHistoryDag (class in historydag.mutation_annotated_dag) AmbiguousLeafSequenceHistoryDag (class in historydag.sequence_dag) apply_muts() (historydag.compact_genome.CompactGenome method) apply_muts_raw() (historydag.compact_genome.CompactGenome method) ascii_compare_histories() (in module historydag.dag) average_pairwise_rf_distance() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

B

binary_support() (in module historydag.utils) build_dag_from_trees() (in module historydag.parsimony)

build_tree() (in module historydag.parsimony) build_trees_from_files() (in module historydag.parsimony)

C

cartesian_product() (in module historydag.utils) cg_diff() (in module historydag.compact_genome) CGHistoryDag (class in historydag.mutation_annotated_dag) character_distance() (historydag.parsimony_utils.SitewiseTransitionModel method) (historydag.parsimony_utils.TransitionModel method) (historydag.parsimony_utils.UnitTransitionModel method) child_clades() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) children() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) clade_union() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) collapse_adjacent_sequences() (in module historydag.utils) compact_genome_from_sequence() (in module historydag.compact_genome) compact_genome_hamming_distance_countfuncs (in module historydag.parsimony_utils) CompactGenome (class in historydag.compact_genome) convert() (in module historydag.dag) convert_to_collapsed() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) copy() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_edges() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

count_histories() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_labeled_binary_topologies() (in module historydag.utils) count_nodes() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_optimal_histories() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_paths_to_leaf() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_resolved_clade_supports() (in module historydag.utils) count_rf_distances() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_sum_rf_distances() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_topologies() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_topologies_fast() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) count_trees() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) counter_prod() (in module historydag.counterops) counter_sum() (in module historydag.counterops)

D

DecimalState (class in historydag.utils) default() (historydag.mutation_annotated_dag.HDagJSONEncoder method) default_nt_gaps_transitions (in module historydag.parsimony_utils)

default_nt_transitions (in module historydag.parsimony_utils) disambiguate() (in module historydag.parsimony) disambiguate_history() (in module historydag.parsimony)

E

edge_difference_funcs() (in module historydag.utils) EdgeSet (class in historydag.dag_node) empty_copy() (historydag.dag_node.HistoryDagNode method) (historydag.dag_node.UANode method) (historydag.HistoryDagNode method) empty_node() (in module historydag) (in module historydag.dag_node)

EteTreeBuilder (class in historydag.dag) explode_label() (in module historydag.utils) explode_nodes() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) export_edge_probabilities() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

F

fast_sample() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) find_node() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) find_nodes() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) flatten() (historydag.mutation_annotated_dag.CGHistoryDag method)

FloatState (class in historydag.utils) from_history_dag() (historydag.dag.HistoryDag class method) (historydag.HistoryDag class method) from_newick() (in module historydag) (in module historydag.dag) from_tree() (in module historydag) (in module historydag.dag)

G

get_adjacency_array() (historydag.parsimony_utils.SitewiseTransitionModel method) (historydag.parsimony_utils.TransitionModel method) get_ambiguity_from_tuple() (historydag.parsimony_utils.TransitionModel method) get_annotated_edges() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_edges() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_finished_tree() (historydag.dag.PreorderTreeBuilder method) get_histories() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_histories_by_index() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_label_type() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_leaves() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

get_probability_countfuncs() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_reference_sequence() (historydag.mutation_annotated_dag.CGHistoryDag method) get_sequence_resolution_count_func() (historydag.parsimony_utils.AmbiguityMap method) get_sequence_resolution_func() (historydag.parsimony_utils.AmbiguityMap method) get_site() (historydag.compact_genome.CompactGenome method) get_topologies() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_trees() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) get_weighted_cg_parsimony_countfuncs() (historydag.parsimony_utils.TransitionModel method) (historydag.parsimony_utils.UnitTransitionModel method) get_weighted_parsimony_countfuncs() (historydag.parsimony_utils.TransitionModel method) (historydag.parsimony_utils.UnitTransitionModel method)

H

hamming_cg_edge_weight() (in module historydag.parsimony_utils) hamming_cg_edge_weight_ambiguous_leaves() (in module historydag.parsimony_utils) hamming_distance_countfuncs (in module historydag.parsimony_utils) hamming_edge_weight() (in module historydag.parsimony_utils) hamming_edge_weight_ambiguous_leaves() (in module historydag.parsimony_utils) hamming_parsimony_count() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) (historydag.mutation_annotated_dag.AmbiguousLeafCGHistoryDag method) (historydag.mutation_annotated_dag.CGHistoryDag method) (historydag.sequence_dag.AmbiguousLeafSequenceHistoryDag method) (historydag.sequence_dag.SequenceHistoryDag method) HDagJSONEncoder (class in historydag.mutation_annotated_dag) hist() (in module historydag.utils) history_dag_from_clade_trees() (in module historydag.dag) history_dag_from_etes() (in module historydag) (in module historydag.dag) history_dag_from_histories() (in module historydag) (in module historydag.dag) history_dag_from_newicks() (in module historydag) (in module historydag.dag) history_dag_from_nodes() (in module historydag.dag) history_dag_from_trees() (in module historydag.dag) history_intersect() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

HistoryDag (class in historydag) (class in historydag.dag) historydag.compact_genome module historydag.counterops module historydag.dag module historydag.dag_node module historydag.mutation_annotated_dag module historydag.parsimony module historydag.parsimony_utils module historydag.sequence_dag module historydag.utils module HistoryDagFilter (class in historydag.utils) HistoryDagNode (class in historydag) (class in historydag.dag_node)

I

ignore_uanode() (in module historydag.utils) insert_node() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) internal_avg_parents() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) IntersectionError IntState (class in historydag.utils) is_ambiguous() (historydag.parsimony_utils.AmbiguityMap method) is_clade_tree() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) is_collapsed() (in module historydag.utils) is_history() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

is_history_root() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) is_leaf() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) is_root() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) is_ua_node() (historydag.dag_node.HistoryDagNode method) (historydag.dag_node.UANode method) (historydag.HistoryDagNode method) iter_covering_histories() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) iter_resolved_clade_supports() (in module historydag.utils)

L

label_uncertainty_summary() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) leaf_ambiguous_compact_genome_hamming_distance_countfuncs (in module historydag.parsimony_utils) leaf_ambiguous_hamming_distance_countfuncs (in module historydag.parsimony_utils) leaf_path_uncertainty_dag() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) leaf_path_uncertainty_graphviz() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

linear_combination() (historydag.utils.AddFuncDict method) load_fasta() (in module historydag.utils) load_json_file() (in module historydag.mutation_annotated_dag) load_MAD_protobuf() (in module historydag.mutation_annotated_dag) load_MAD_protobuf_file() (in module historydag.mutation_annotated_dag) log_natural_probability_funcs (in module historydag.utils) logsumexp() (in module historydag.utils)

M

make_binary_complete_dag() (in module historydag.dag) make_complete() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) make_newickcountfuncs() (in module historydag.utils) make_rfdistance_countfuncs() (in module historydag.utils) make_uniform() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) make_weighted_hamming_count_funcs() (in module historydag.parsimony) mask_sites() (historydag.compact_genome.CompactGenome method) merge() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) min_character_distance() (historydag.parsimony_utils.TransitionModel method) min_character_mutation() (historydag.parsimony_utils.SitewiseTransitionModel method) (historydag.parsimony_utils.TransitionModel method) (historydag.parsimony_utils.UnitTransitionModel method) min_weighted_cg_hamming_distance() (historydag.parsimony_utils.TransitionModel method)

min_weighted_cg_hamming_edge_weight() (historydag.parsimony_utils.TransitionModel method) min_weighted_hamming_distance() (historydag.parsimony_utils.TransitionModel method) min_weighted_hamming_edge_weight() (historydag.parsimony_utils.TransitionModel method) module historydag.compact_genome historydag.counterops historydag.dag historydag.dag_node historydag.mutation_annotated_dag historydag.parsimony historydag.parsimony_utils historydag.sequence_dag historydag.utils most_supported_trees() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) mutate() (historydag.compact_genome.CompactGenome method) mutations_as_strings() (historydag.compact_genome.CompactGenome method)

N

natural_distribution_annotate() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) natural_edge_probability() (in module historydag.utils) node_countfuncs (in module historydag.utils) node_probabilities() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) node_self() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method)

NodeIDHistoryDag (class in historydag.mutation_annotated_dag) nodes_above_node() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) num_edges() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) num_leaves() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) num_nodes() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

O

optimal_rf_distance() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) optimal_sum_rf_distance() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

optimal_weight_annotate() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) overestimate_rf_diameter() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

P

parsimony_score() (in module historydag.parsimony) parsimony_scores_from_files() (in module historydag.parsimony) parsimony_scores_from_topologies() (in module historydag.parsimony) partitions() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) postorder() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) postorder_above() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) postorder_cladetree_accum() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

postorder_history_accum() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) powerset() (in module historydag.utils) preorder() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) preorder_history_accum() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) PreorderHistoryBuilder (class in historydag.dag) PreorderTreeBuilder (class in historydag.dag) probability_annotate() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) prod() (in module historydag.utils)

R

read_alignment() (in module historydag.compact_genome) read_fasta() (in module historydag.utils) recompute_parents() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) reconcile_cgs() (in module historydag.compact_genome) relabel() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

remove_invariant_sites() (in module historydag.parsimony) remove_label_fields() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) remove_node() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) remove_sites() (historydag.compact_genome.CompactGenome method) replace_label_attr() (in module historydag.parsimony) ReversedAmbiguityMap (class in historydag.parsimony_utils)

S

sample() (historydag.dag.HistoryDag method) (historydag.dag_node.EdgeSet method) (historydag.HistoryDag method) sample_with_edge() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) sample_with_node() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) sankoff_downward() (in module historydag.parsimony) sankoff_postorder_iter_accum() (in module historydag.parsimony) sankoff_upward() (in module historydag.parsimony) sequence_resolution_count() (historydag.parsimony_utils.AmbiguityMap method) sequence_resolutions() (historydag.parsimony_utils.AmbiguityMap method) SequenceHistoryDag (class in historydag.sequence_dag) set_edge_stats() (historydag.dag_node.EdgeSet method) set_sample_mask() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) set_targets() (historydag.dag_node.EdgeSet method) shallowcopy() (historydag.dag_node.EdgeSet method) shared_history_count() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) SitewiseTransitionModel (class in historydag.parsimony_utils)

sorted_child_clades() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) sorted_partitions() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) standard_nt_ambiguity_map (in module historydag.parsimony_utils) standard_nt_ambiguity_map_gap_as_char (in module historydag.parsimony_utils) StrState (class in historydag.utils) subset_sites() (historydag.compact_genome.CompactGenome method) sum_probability() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) sum_rf_distances() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) sum_rfdistance_funcs() (in module historydag.utils) sum_weights() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) summary() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) (historydag.mutation_annotated_dag.AmbiguousLeafCGHistoryDag method) (historydag.mutation_annotated_dag.CGHistoryDag method) (historydag.sequence_dag.AmbiguousLeafSequenceHistoryDag method) (historydag.sequence_dag.SequenceHistoryDag method) superset_sites() (historydag.compact_genome.CompactGenome method)

T

TaxaError test_equal() (historydag.mutation_annotated_dag.CGHistoryDag method) to_ascii() (historydag.dag.HistoryDag method) (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDag method) (historydag.HistoryDagNode method) to_ete() (historydag.dag.HistoryDag method) (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDag method) (historydag.HistoryDagNode method) to_graphviz() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) to_json() (historydag.mutation_annotated_dag.CGHistoryDag method) to_json_file() (historydag.mutation_annotated_dag.CGHistoryDag method) to_newick() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

to_newicks() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) to_protobuf() (historydag.mutation_annotated_dag.CGHistoryDag method) to_protobuf_file() (historydag.mutation_annotated_dag.CGHistoryDag method) to_sequence() (historydag.compact_genome.CompactGenome method) TransitionModel (class in historydag.parsimony_utils) treewise_sankoff_in_dag() (in module historydag.parsimony) trim_below_weight() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) trim_optimal_rf_distance() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) trim_optimal_sum_rf_distance() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) trim_optimal_weight() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) trim_topology() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

U

UALabel (class in historydag.utils) UANode (class in historydag.dag_node) under_clade() (historydag.dag_node.HistoryDagNode method) (historydag.HistoryDagNode method) underestimate_rf_diameter() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) unflatten() (in module historydag.mutation_annotated_dag)

uniform_distribution_annotate() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) UnitTransitionModel (class in historydag.parsimony_utils) unlabel() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) unpack_mut_string() (in module historydag.compact_genome) update_label_fields() (historydag.dag.HistoryDag method) (historydag.HistoryDag method)

W

weight_count() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) weight_counts_with_ambiguities() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) (historydag.mutation_annotated_dag.CGHistoryDag method)

weight_range_annotate() (historydag.dag.HistoryDag method) (historydag.HistoryDag method) weighted_cg_hamming_distance() (historydag.parsimony_utils.TransitionModel method) weighted_cg_hamming_edge_weight() (historydag.parsimony_utils.TransitionModel method) weighted_hamming_distance() (historydag.parsimony_utils.TransitionModel method) weighted_hamming_edge_weight() (historydag.parsimony_utils.TransitionModel method)