Index

A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | W

A

add_child() (TreeNode method)
add_face() (FaceContainer method)
(TreeNode method)
add_face_to_node() (in module ete2)
add_feature() (TreeNode method)
add_features() (TreeNode method)
add_sister() (TreeNode method)
annotate_ncbi_taxa() (PhyloNode method)
annotate_tree() (NCBITaxa method)
AttrFace (class in ete2)

B

BarChartFace (class in ete2)
build_from_file() (Nexml method)

C

change_dist_to_evol() (EvolNode method)
check_monophyly() (TreeNode method)
children (TreeNode attribute)
CircleFace (class in ete2)
ClusterNode (class in ete2)
ClusterTree (in module ete2)
collapse_lineage_specific_expansions() (PhyloNode method)
COLOR_SCHEMES (in module ete2)
compare() (TreeNode method)
convert_to_ultrametric() (TreeNode method)
copy() (TreeNode method)
count_algs() (PhylomeDB3Connector method)
count_trees() (PhylomeDB3Connector method)

D

del_feature() (TreeNode method)
delete() (TreeNode method)
describe() (TreeNode method)
detach() (TreeNode method)
dist (TreeNode attribute)
DynamicItemFace (class in ete2)

E

ete2 (module), [1]
ete2.clustering (module), [1]
ete2.evol (module)
ete2.ncbi_taxonomy (module)
ete2.nexml (module)
ete2.parser.seqgroup (module)
ete2.phylo (module)
ete2.phyloxml (module)
ete2.treeview (module)
ete2.webplugin (module), [1]
EvolEvent (class in ete2.phylo)
EvolNode (class in ete2)
EvolTree (in module ete2)
expand_polytomies() (TreeNode method)

F

Face (class in ete2)
FaceContainer (class in ete2)

G

get_age() (PhyloNode method)
get_age_balanced_outgroup() (PhyloNode method)
get_algs() (PhylomeDB3Connector method)
get_all_isoforms() (PhylomeDB3Connector method)
get_ancestors() (TreeNode method)
get_ascii() (TreeNode method)
get_available_trees_by_phylome() (PhylomeDB3Connector method)
get_best_tree() (PhylomeDB3Connector method)
get_broken_branches() (NCBITaxa method)
get_cached_content() (TreeNode method)
get_children() (TreeNode method)
get_clean_alg() (PhylomeDB3Connector method)
get_closest_leaf() (TreeNode method)
get_collateral_seeds() (PhylomeDB3Connector method)
get_common_ancestor() (TreeNode method)
get_descendant_by_node_id() (EvolNode method)
get_descendant_evol_events() (PhyloNode method)
get_descendants() (TreeNode method)
get_distance() (TreeNode method)
get_dunn() (ClusterNode method)
get_edges() (TreeNode method)
get_entries() (SeqGroup method)
get_evol_model() (EvolNode method)
get_external_ids() (PhylomeDB3Connector method)
get_farthest_leaf() (TreeNode method)
get_farthest_node() (TreeNode method)
get_farthest_oldest_leaf() (PhyloNode method)
get_farthest_oldest_node() (PhyloNode method)
get_fuzzy_name_translation() (NCBITaxa method)
get_genome_ids() (PhylomeDB3Connector method)
get_genome_info() (PhylomeDB3Connector method)
get_genomes() (PhylomeDB3Connector method)
get_genomes_by_species() (PhylomeDB3Connector method)
get_go_ids() (PhylomeDB3Connector method)
get_id_by_external() (PhylomeDB3Connector method)
get_id_translations() (PhylomeDB3Connector method)
get_info_homologous_seqs() (PhylomeDB3Connector method)
get_leaf_names() (TreeNode method)
get_leaf_profiles() (ClusterNode method)
get_leaves() (TreeNode method)
get_leaves_by_name() (TreeNode method)
get_lineage() (NCBITaxa method)
get_longest_isoform() (PhylomeDB3Connector method)
get_midpoint_outgroup() (TreeNode method)
get_monophyletic() (TreeNode method)
get_most_likely() (EvolNode method)
get_my_evol_events() (PhyloNode method)
get_name_translator() (NCBITaxa method)
get_new_phylomedb_id() (PhylomeDB3Connector method)
get_old_phylomedb_ids() (PhylomeDB3Connector method)
get_phylome_algs() (PhylomeDB3Connector method)
get_phylome_info() (PhylomeDB3Connector method)
get_phylome_seed_ids() (PhylomeDB3Connector method)
get_phylome_seed_ids_info() (PhylomeDB3Connector method)
get_phylome_trees() (PhylomeDB3Connector method)
get_phylomes() (PhylomeDB3Connector method)
get_phylomes_for_seed_ids() (PhylomeDB3Connector method)
get_prot_gene_names() (PhylomeDB3Connector method)
get_proteomes_in_phylome() (PhylomeDB3Connector method)
get_rank() (NCBITaxa method)
get_raw_alg() (PhylomeDB3Connector method)
get_seq() (SeqGroup method)
get_seq_info_in_tree() (PhylomeDB3Connector method)
get_seq_info_msf() (PhylomeDB3Connector method)
get_seqid_info() (PhylomeDB3Connector method)
get_seqs_in_genome() (PhylomeDB3Connector method)
get_silhouette() (ClusterNode method)
get_sisters() (TreeNode method)
get_speciation_trees() (PhyloNode method)
get_species() (PhylomeDB3Connector method)
(PhyloNode method)
get_species_in_phylome() (PhylomeDB3Connector method)
get_species_info() (PhylomeDB3Connector method)
get_taxid_translator() (NCBITaxa method)
get_topology() (NCBITaxa method)
get_topology_id() (TreeNode method)
get_tree() (PhylomeDB3Connector method)
get_tree_root() (TreeNode method)

H

hoverEnterEvent() (SequenceFace.InteractiveLetterItem method)
hoverLeaveEvent() (SequenceFace.InteractiveLetterItem method)

I

img_style (TreeNode attribute)
ImgFace (class in ete2)
is_leaf() (TreeNode method)
is_root() (TreeNode method)
iter_ancestors() (TreeNode method)
iter_descendants() (TreeNode method)
iter_edges() (TreeNode method)
iter_entries() (SeqGroup method)
iter_leaf_names() (TreeNode method)
iter_leaf_profiles() (ClusterNode method)
iter_leaves() (TreeNode method)
iter_prepostorder() (TreeNode method)
iter_search_nodes() (TreeNode method)
iter_species() (PhyloNode method)

L

ladderize() (TreeNode method)
link_to_alignment() (EvolNode method)
(PhyloNode method)
link_to_arraytable() (ClusterNode method)
link_to_evol_model() (EvolNode method)

M

mark_tree() (EvolNode method)

N

ncbi_compare() (PhyloNode method)
NCBITaxa (class in ete2)
Nexml (class in ete2)
NexmlTree (class in ete2)
NodeStyle (class in ete2)

P

PhylomeDB3Connector (class in ete2)
PhyloNode (class in ete2)
PhyloTree (in module ete2)
Phyloxml (class in ete2)
PhyloxmlTree (class in ete2)
PieChartFace (class in ete2)
populate() (TreeNode method)
ProfileFace (class in ete2)
prune() (TreeNode method)

R

random_color() (in module ete2)
reconcile() (PhyloNode method)
RectFace (class in ete2)
register_action() (WebTreeApplication method)
remove_child() (TreeNode method)
remove_sister() (TreeNode method)
render() (EvolNode method)
(TreeNode method)
resolve_polytomy() (TreeNode method)
robinson_foulds() (TreeNode method)
run_model() (EvolNode method)

S

search_id() (PhylomeDB3Connector method)
search_nodes() (TreeNode method)
sep (EvolNode attribute)
SeqGroup (class in ete2)
SeqMotifFace (class in ete2)
SequenceFace (class in ete2)
SequenceFace.InteractiveLetterItem (class in ete2)
set_default_layout_fn() (WebTreeApplication method)
set_distance_function() (ClusterNode method)
set_external_app_handler() (WebTreeApplication method)
set_external_tree_renderer() (WebTreeApplication method)
set_outgroup() (TreeNode method)
set_seq() (SeqGroup method)
set_species_naming_function() (PhyloNode method)
set_style() (TreeNode method)
set_tree_loader() (WebTreeApplication method)
set_tree_size() (WebTreeApplication method)
set_tree_style() (WebTreeApplication method)
show() (EvolNode method)
(TreeNode method)
sort_descendants() (TreeNode method)
species (PhyloNode attribute)
split_by_dups() (PhyloNode method)
StackedBarFace (class in ete2)
standardize() (TreeNode method)
StaticItemFace (class in ete2)
support (TreeNode attribute)
SVG_COLORS (in module ete2)
swap_children() (TreeNode method)

T

TextFace (class in ete2)
translate_to_names() (NCBITaxa method)
traverse() (TreeNode method)
Tree (in module ete2)
TreeFace (class in ete2)
TreeNode (class in ete2)
TreeStyle (class in ete2)

U

unroot() (TreeNode method)
up (TreeNode attribute)
update_taxonomy_database() (NCBITaxa method)

W

WebTreeApplication (class in ete2)
write() (EvolNode method)
(SeqGroup method)
(TreeNode method)