Index
A
|
B
|
C
|
D
|
E
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
A
add_pair() (phylonetwork.PhylogeneticNetwork method)
add_sequence() (phylonetwork.PhylogeneticNetwork method)
all_binary_trees_by_num_taxa() (in module phylonetwork.tree_generators)
all_binary_trees_by_taxa() (in module phylonetwork.tree_generators)
all_sequences (phylonetwork.PhylogeneticNetwork attribute)
all_sequences_array (phylonetwork.PhylogeneticNetwork attribute)
all_trees() (in module phylonetwork.tree_generators)
B
bottom_to_top_nodes (phylonetwork.NetworkShape attribute)
C
cached_taxa (phylonetwork.PhylogeneticNetwork attribute)
cherry() (phylonetwork.PhylogeneticNetwork method)
clear_cache() (in module phylonetwork.utils)
(phylonetwork.NetworkShape method)
clear_cached_taxa() (phylonetwork.PhylogeneticNetwork method)
clearable_cached_property (class in phylonetwork.utils)
cluster() (phylonetwork.PhylogeneticNetwork method)
cluster_dict (phylonetwork.PhylogeneticNetwork attribute)
cophenetic_matrix() (phylonetwork.PhylogeneticTree method)
D
delta() (phylonetwork.PhylogeneticNetwork method)
depths (phylonetwork.NetworkShape attribute)
distance() (phylonetwork.PhylogeneticNetwork method)
draw() (phylonetwork.LGTNetwork method)
(phylonetwork.PhylogeneticNetwork method)
E
elementary_nodes (phylonetwork.NetworkShape attribute)
emu() (phylonetwork.PhylogeneticNetwork method)
emu_dict (phylonetwork.PhylogeneticNetwork attribute)
emu_representation (phylonetwork.PhylogeneticNetwork attribute)
eNewick() (phylonetwork.PhylogeneticNetwork method)
entropy() (in module phylonetwork.balances)
extended_sackin() (in module phylonetwork.balances)
H
has_nested_taxa() (phylonetwork.PhylogeneticNetwork method)
heights (phylonetwork.NetworkShape attribute)
hold_and_hang() (in module phylonetwork.tree_operations)
hold_and_label() (in module phylonetwork.tree_operations)
hybridize() (in module phylonetwork.btctc_generators)
I
interior_nodes (phylonetwork.NetworkShape attribute)
is_elementary() (phylonetwork.NetworkShape method)
is_labeled() (phylonetwork.PhylogeneticNetwork method)
is_leaf() (phylonetwork.NetworkShape method)
is_orchard() (phylonetwork.PhylogeneticNetwork method)
is_reticulation() (phylonetwork.NetworkShape method)
is_root() (phylonetwork.NetworkShape method)
is_tree_child() (phylonetwork.PhylogeneticNetwork method)
is_tree_node() (phylonetwork.NetworkShape method)
is_unlabeled_elementary_or_leaf() (phylonetwork.PhylogeneticNetwork method)
L
label() (phylonetwork.PhylogeneticNetwork method)
labeled_nodes (phylonetwork.PhylogeneticNetwork attribute)
labeling_dict (phylonetwork.PhylogeneticNetwork attribute)
LCA() (phylonetwork.PhylogeneticTree method)
LCA_dict (phylonetwork.PhylogeneticTree attribute)
leaves (phylonetwork.NetworkShape attribute)
level() (phylonetwork.NetworkShape method)
LGTNetwork (class in phylonetwork)
lookup_label_dict (phylonetwork.PhylogeneticNetwork attribute)
M
make_elementary_node() (phylonetwork.NetworkShape method)
MalformedNewickException
mu() (phylonetwork.PhylogeneticNetwork method)
mu_dict (phylonetwork.PhylogeneticNetwork attribute)
N
nested_label() (phylonetwork.PhylogeneticNetwork method)
nested_label_dict (phylonetwork.PhylogeneticNetwork attribute)
NetworkShape (class in phylonetwork)
new_node() (phylonetwork.NetworkShape method)
new_reticulation_node() (phylonetwork.NetworkShape method)
nodal_matrix() (phylonetwork.PhylogeneticTree method)
node_with_label() (phylonetwork.PhylogeneticNetwork method)
NotAPhylogeneticNetwork
NotImplemented
number_of_trees() (in module phylonetwork.tree_generators)
O
ordered_cached_taxa (phylonetwork.PhylogeneticNetwork attribute)
ordered_taxa (phylonetwork.PhylogeneticNetwork attribute)
P
parent() (phylonetwork.PhylogeneticNetwork method)
PhylogeneticNetwork (class in phylonetwork)
PhylogeneticTree (class in phylonetwork)
phylonetwork (module)
phylonetwork.balances (module)
phylonetwork.btctc_generators (module)
phylonetwork.exceptions (module)
phylonetwork.tree_generators (module)
phylonetwork.tree_operations (module)
phylonetwork.utils (module)
principal_edges() (phylonetwork.LGTNetwork method)
principal_subtree() (phylonetwork.LGTNetwork method)
product() (in module phylonetwork.utils)
push_and_hang() (in module phylonetwork.tree_operations)
push_and_label() (in module phylonetwork.tree_operations)
R
random_combination() (in module phylonetwork.btctc_generators)
random_uniform_tree_generator() (in module phylonetwork.tree_generators)
random_weighted() (in module phylonetwork.utils)
random_yule_btctc_generator() (in module phylonetwork.btctc_generators)
random_yule_tree_generator() (in module phylonetwork.tree_generators)
reduce_pair() (phylonetwork.PhylogeneticNetwork method)
reduce_sequence() (phylonetwork.PhylogeneticNetwork method)
reducible_pairs (phylonetwork.PhylogeneticNetwork attribute)
relabel() (in module phylonetwork.tree_generators)
remove_elementary_nodes() (phylonetwork.NetworkShape method)
remove_node_and_reconnect() (phylonetwork.NetworkShape method)
remove_taxa() (phylonetwork.PhylogeneticNetwork method)
reticulations (phylonetwork.NetworkShape attribute)
root (phylonetwork.NetworkShape attribute)
roots (phylonetwork.NetworkShape attribute)
S
sackin() (in module phylonetwork.balances)
secondary_edges() (phylonetwork.LGTNetwork method)
secondary_subtrees() (phylonetwork.LGTNetwork method)
set_cached_taxa() (phylonetwork.PhylogeneticNetwork method)
smallest_pair (phylonetwork.PhylogeneticNetwork attribute)
smallest_sequence (phylonetwork.PhylogeneticNetwork attribute)
smallest_sequence_array (phylonetwork.PhylogeneticNetwork attribute)
speciate() (in module phylonetwork.btctc_generators)
T
taxa (phylonetwork.PhylogeneticNetwork attribute)
TaxaException
top_to_bottom_nodes (phylonetwork.NetworkShape attribute)
topological_restriction() (phylonetwork.PhylogeneticNetwork method)
tree_nodes (phylonetwork.NetworkShape attribute)
tree_with_single_taxon() (in module phylonetwork.tree_generators)
U
unlabeled_nodes (phylonetwork.PhylogeneticNetwork attribute)
PhyloNetwork
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