Index

A

AF_3Di() (in module evoten.substitution_models)

B

block_layout() (in module evoten.maf)

C

change_root() (evoten.tree_handler.TreeHandler method) close() (evoten.maf.MafWriter method) codon_frequencies() (in module evoten.substitution_models) 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)

device_index() (evoten.tree_handler.TreeHandler method) draw() (evoten.tree_handler.TreeHandler method)

E

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

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

F

finished (evoten.tree_handler.NodeData attribute)

foldseek_3Di() (in module evoten.substitution_models) from_newick() (evoten.tree_handler.TreeHandler class method)

G

genetic_code() (in module evoten.substitution_models) 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) gy94() (in module evoten.substitution_models)

H

height (evoten.tree_handler.NodeData attribute)

I

index (evoten.tree_handler.NodeData attribute)

J

jukes_cantor() (in module evoten.substitution_models)

L

layer_size() (evoten.tree_handler.TreeHandler method) level_routing() (evoten.tree_handler.TreeHandler method)

LG() (in module evoten.substitution_models) loglik() (in module evoten.model)

M

MafWriter (class in evoten.maf) mean_rate() (in module evoten.substitution_models) module evoten evoten.maf evoten.model evoten.substitution_models evoten.tree_handler evoten.util

N

node (evoten.tree_handler.NodeData attribute)

NodeData (class in evoten.tree_handler) nucleotide_gtr() (in module evoten.substitution_models)

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) PRUNING_MODES (in module evoten.model)

R

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

reorder() (evoten.tree_handler.TreeHandler method) routing_for() (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) stratify_branchlen() (evoten.tree_handler.TreeHandler method)

T

to_newick() (evoten.tree_handler.TreeHandler method) TreeHandler (class in evoten.tree_handler) triplet_independent() (in module evoten.substitution_models)

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() (evoten.maf.MafWriter method)

write_maf() (in module evoten.maf) write_rate_model() (in module evoten.util)