Index

A

aa_string() (bte.AAChange method) AAChange (class in bte)

apply_mutations() (bte.MATree method) apply_node_annotations() (bte.MATree method)

B

breadth_first_expansion() (bte.MATree method)

bte module

C

clear() (bte.MATree method) compute_nucleotide_diversity() (bte.MATree method) count_clades_inclusive() (bte.MATree method)

count_haplotypes() (bte.MATree method) count_leaves() (bte.MATree method) count_mutation_types() (bte.MATree method) create_node() (bte.MATree method)

D

depth_first_expansion() (bte.MATree method)

dump_node_annotations() (bte.MATree method)

F

from_json() (bte.MATree method) from_newick() (bte.MATree method)

from_newick_and_vcf() (bte.MATree method) from_newick_string() (bte.MATree method) from_pb() (bte.MATree method)

G

get_annotations() (bte.MATree method) get_clade() (bte.MATree method) get_clade_samples() (bte.MATree method) get_haplotype() (bte.MATree method) get_leaves() (bte.MATree method) get_leaves_ids() (bte.MATree method) get_mutation() (bte.MATree method)

get_mutation_information() (bte.MATNode method) get_mutation_samples() (bte.MATree method) get_newick() (bte.MATree method) get_node() (bte.MATree method) get_parsimony_score() (bte.MATree method) get_random() (bte.MATree method) get_regex() (bte.MATree method) get_regex_samples() (bte.MATree method)

I

is_leaf() (bte.MATNode method)

is_synonymous() (bte.AAChange method)

L

ladderize() (bte.MATree method)

LCA() (bte.MATree method) list_clades() (bte.MATree method)

M

MATNode (class in bte) MATree (class in bte) module bte

most_recent_annotation() (bte.MATNode method) move_node() (bte.MATree method) mutation_set() (bte.MATree method)

R

remove_node() (bte.MATree method) reverse_strand() (bte.MATree method)

root (bte.MATree attribute) rsearch() (bte.MATree method)

S

save_pb() (bte.MATree method) set_branch_length() (bte.MATNode method)

simple_parsimony() (bte.MATree method) subtree() (bte.MATree method)

T

translate() (bte.MATree method)

tree_entropy() (bte.MATree method)

U

update_mutations() (bte.MATNode method)

W

write_json() (bte.MATree method)

write_newick() (bte.MATree method) write_vcf() (bte.MATree method)