Index

A

all_splits() (in module splitp.splits)

ASCII (splitp.enums.DrawFormat attribute)

B

balanced_newick_tree() (in module splitp.trees)

D

distance (splitp.enums.Method attribute) distance_matrix() (in module splitp.phylogenetics)

draw() (splitp.phylogeny.Phylogeny method) draw_from_multinomial() (in module splitp.simulation) DrawFormat (class in splitp.enums)

E

erickson_SVD() (in module splitp.phylogenetics) euclidean_split_distance() (in module splitp.phylogenetics)

evaluate_polynomial() (splitp.squangles.SquangleEvaluator method) evolve_pattern() (in module splitp.simulation)

F

fasta_to_dict() (in module splitp.parsers.fasta) FlatFormat (class in splitp.enums) flattening (splitp.enums.Method attribute) flattening() (in module splitp.constructions)

flattening_rank_1_approximation() (in module splitp.phylogenetics) flattening_rank_1_approximation_divergence() (in module splitp.phylogenetics) format_split() (in module splitp.splits) (splitp.phylogeny.Phylogeny method) frobenius_norm() (in module splitp.matrix)

G

generate_alignment() (in module splitp.simulation) get_descendants() (splitp.phylogeny.Phylogeny method) get_num_nodes() (splitp.phylogeny.Phylogeny method) get_num_taxa() (splitp.phylogeny.Phylogeny method) get_parent() (splitp.phylogeny.Phylogeny method)

get_pattern_counts() (in module splitp.parsers.fasta) get_pattern_probabilities() (in module splitp.simulation) get_polynomials() (splitp.squangles.SquangleEvaluator method) get_taxa() (splitp.phylogeny.Phylogeny method) GTR (class in splitp.model)

H

hartigan_algorithm() (in module splitp.phylogenetics)

I

is_leaf() (splitp.phylogeny.Phylogeny method)

is_root() (splitp.phylogeny.Phylogeny method) is_sparse() (in module splitp.matrix)

J

JC (splitp.enums.Model attribute) JC_corrected_distance_matrix() (in module splitp.phylogenetics)

join_nodes() (in module splitp.phylogenetics) json_to_newick() (in module splitp.parsers.newick) JukesCantor() (splitp.model.GTR class method)

K

K2ST (splitp.enums.Model attribute)

Kimura() (splitp.model.GTR class method)

M

matplotlib (splitp.enums.DrawFormat attribute) Method (class in splitp.enums) midpoint_rooting() (in module splitp.phylogenetics) Model (class in splitp.enums) model (class in splitp.model) module splitp splitp.constants splitp.constructions splitp.enums splitp.matrix splitp.model splitp.parsers splitp.parsers.fasta splitp.parsers.newick splitp.phylogenetics splitp.phylogeny splitp.simulation splitp.splits splitp.squangles splitp.trees

move_tree_edge_labels_to_nodes() (in module splitp.parsers.newick) mutual_information (splitp.enums.Method attribute)

N

name (splitp.phylogeny.Phylogeny attribute) neighbour_joining() (in module splitp.phylogenetics) networkx_graph (splitp.phylogeny.Phylogeny attribute) newick_string (splitp.phylogeny.Phylogeny attribute)

newick_string_from_splits() (in module splitp.phylogenetics) newick_to_json() (in module splitp.parsers.newick) node_index() (splitp.phylogeny.Phylogeny method) nodes() (splitp.phylogeny.Phylogeny method)

P

parsimony_score() (in module splitp.phylogenetics) pattern_counts_to_probs() (in module splitp.parsers.fasta)

pattern_probs_from_alignment() (in module splitp.parsers.fasta) Phylogeny (class in splitp.phylogeny)

R

read_alignment_from_file() (in module splitp.parsers.fasta) read_polynomial() (splitp.squangles.SquangleEvaluator method)

reassign_transition_matrices() (splitp.phylogeny.Phylogeny method) reduced (splitp.enums.FlatFormat attribute) root() (splitp.phylogeny.Phylogeny method)

S

shuffle() (in module splitp.splits) sparse (splitp.enums.FlatFormat attribute) split_balance() (in module splitp.splits) split_score() (in module splitp.phylogenetics) split_tree_parsimony() (in module splitp.phylogenetics) splitp module splitp.constants module splitp.constructions module splitp.enums module splitp.matrix module splitp.model module splitp.parsers module splitp.parsers.fasta module

splitp.parsers.newick module splitp.phylogenetics module splitp.phylogeny module splitp.simulation module splitp.splits module splitp.squangles module splitp.trees module splits() (splitp.phylogeny.Phylogeny method) SquangleEvaluator (class in splitp.squangles) star_tree() (in module splitp.phylogenetics) strip_newick() (in module splitp.parsers.newick) subflattening (splitp.enums.Method attribute) subflattening() (in module splitp.constructions)

T

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

transformed_prob_dist() (splitp.squangles.SquangleEvaluator method) transition_matrix() (splitp.model.model method) tree_from_splits() (in module splitp.phylogenetics)

U

unrooted_networkx_graph() (splitp.phylogeny.Phylogeny method)