Index

C

change_root() (evoten.tree_handler.TreeHandler method) collapse() (evoten.tree_handler.TreeHandler method) compute_ancestral_marginals() (in module evoten.model)

compute_ancestral_probabilities() (in module evoten.model) compute_leaf_out_marginals() (in module evoten.model) copy() (evoten.tree_handler.TreeHandler class method)

D

data_path() (in module evoten.util)

draw() (evoten.tree_handler.TreeHandler method)

E

encode_one_hot() (in module evoten.util) encode_tuple_alignment() (in module evoten.util) evoten module evoten.model module

evoten.substitution_models module evoten.tree_handler module evoten.util module

F

finished (evoten.tree_handler.NodeData attribute)

from_newick() (evoten.tree_handler.TreeHandler class method)

G

get_branch_lengths_by_height() (evoten.tree_handler.TreeHandler method) get_index() (evoten.tree_handler.TreeHandler method) get_indices() (evoten.tree_handler.TreeHandler method)

get_internal_counts_by_height() (evoten.tree_handler.TreeHandler method) get_leaf_counts_by_height() (evoten.tree_handler.TreeHandler method) get_parent_indices_by_height() (evoten.tree_handler.TreeHandler method) get_values_by_height() (evoten.tree_handler.TreeHandler method)

H

height (evoten.tree_handler.NodeData attribute)

I

index (evoten.tree_handler.NodeData attribute)

J

jukes_cantor() (in module evoten.substitution_models)

L

LG() (in module evoten.substitution_models)

loglik() (in module evoten.model)

M

module evoten evoten.model evoten.substitution_models evoten.tree_handler evoten.util

N

node (evoten.tree_handler.NodeData attribute)

NodeData (class in evoten.tree_handler)

P

parent (evoten.tree_handler.NodeData attribute) parse_rate_model() (in module evoten.util) permute_rate_model() (in module evoten.util)

print_tuple_rate_matrix() (in module evoten.util) print_tuple_stationary() (in module evoten.util) propagate() (in module evoten.model) prune() (evoten.tree_handler.TreeHandler method)

R

read() (evoten.tree_handler.TreeHandler class method)

reorder() (evoten.tree_handler.TreeHandler method)

S

set_branch_lengths() (evoten.tree_handler.TreeHandler method)

setup_init_branch_lengths() (evoten.tree_handler.TreeHandler method) split() (evoten.tree_handler.TreeHandler method)

T

to_newick() (evoten.tree_handler.TreeHandler method) TreeHandler (class in evoten.tree_handler)

tuple_alignment() (in module evoten.util) tuple_array() (in module evoten.util) tuple_labels() (in module evoten.util)

U

update() (evoten.tree_handler.TreeHandler method)

W

write_rate_model() (in module evoten.util)