Index

A

add_node() (splitp.nx_tree.NXTree method) adjacency_matrix() (splitp.nx_tree.NXTree method)

all_singular_values() (splitp.nx_tree.NXTree method) all_splits() (in module splitp.tree_helper_functions) (splitp.nx_tree.NXTree method)

B

balanced_newick_tree() (in module splitp.tree_helper_functions)

build_JC_matrix() (splitp.nx_tree.NXTree method) build_K2ST_matrix() (splitp.nx_tree.NXTree method)

C

check_splits_representatives() (in module splitp.tree_helper_functions)

D

draw_from_multinomial() (splitp.nx_tree.NXTree method)

E

evaluate_polynomial() (splitp.squangles.SquangleEvaluator method)

evolve_pattern() (splitp.nx_tree.NXTree method)

F

false_splits() (splitp.nx_tree.NXTree method) fast_signed_sum_subflattening() (splitp.nx_tree.NXTree method)

fast_sparse_flattening() (splitp.nx_tree.NXTree method) flattening() (splitp.nx_tree.NXTree method) frob_norm() (in module splitp.tree_helper_functions)

G

generate_alignment() (splitp.nx_tree.NXTree method) get_balance() (in module splitp.tree_helper_functions) get_descendants() (splitp.nx_tree.NXTree method) get_flattening() (splitp.squangles.SquangleEvaluator method) get_num_taxa() (splitp.nx_tree.NXTree method)

get_parent() (splitp.nx_tree.NXTree method) get_pattern_counts() (in module splitp.tree_helper_functions) get_pattern_probabilities() (splitp.nx_tree.NXTree method) get_polynomials() (splitp.squangles.SquangleEvaluator method) get_root() (splitp.nx_tree.NXTree method)

H

hartigan_algorithm() (splitp.nx_tree.NXTree method)

I

index_of_node() (splitp.nx_tree.NXTree method) is_leaf() (splitp.nx_tree.NXTree method)

is_root() (splitp.nx_tree.NXTree method) is_sparse() (in module splitp.tree_helper_functions)

J

json_to_newick() (in module splitp.parsers)

M

make_substitution_matrix() (in module splitp.tree_helper_functions) module splitp splitp.nx_tree splitp.parsers splitp.squangles splitp.tree_helper_functions

N

newick_to_json() (in module splitp.parsers) node_index() (splitp.nx_tree.NXTree method) node_name() (splitp.nx_tree.NXTree method) nodes() (splitp.nx_tree.NXTree method)

nodes_list() (splitp.nx_tree.NXTree method) normalised() (in module splitp.tree_helper_functions) num_nodes() (splitp.nx_tree.NXTree method) NXTree (class in splitp.nx_tree)

P

parsimony_score() (splitp.nx_tree.NXTree method)

pattern_counts_to_probs() (in module splitp.tree_helper_functions) pattern_probs_from_alignment() (in module splitp.tree_helper_functions)

R

rate_matrix() (splitp.nx_tree.NXTree method) read_alignment_from_file() (in module splitp.tree_helper_functions)

read_polynomial() (splitp.squangles.SquangleEvaluator method) reassign_all_transition_matrices() (splitp.nx_tree.NXTree method)

S

scale_TR_rate_matrix() (splitp.nx_tree.NXTree method) scaled_h_matrix() (in module splitp.tree_helper_functions) scores_to_weights() (in module splitp.tree_helper_functions) signed_sum_subflattening() (splitp.nx_tree.NXTree method) sparse_flattening() (splitp.nx_tree.NXTree method) sparse_subflattening() (splitp.nx_tree.NXTree method) split_equivalence_classes() (in module splitp.tree_helper_functions) split_score() (splitp.nx_tree.NXTree method) splitp module splitp.nx_tree module

splitp.parsers module splitp.squangles module splitp.tree_helper_functions module SquangleEvaluator (class in splitp.squangles) subflattening() (splitp.nx_tree.NXTree method) subflattening_alt() (splitp.nx_tree.NXTree method) svd_error() (splitp.nx_tree.NXTree method)

T

test_pattern_conversion() (splitp.squangles.SquangleEvaluator method) to_int() (splitp.squangles.SquangleEvaluator method) to_pattern() (splitp.squangles.SquangleEvaluator method)

transformed_flattening() (splitp.nx_tree.NXTree method) transformed_prob_dist() (splitp.squangles.SquangleEvaluator method) true_splits() (splitp.nx_tree.NXTree method)