Index

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)

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_ancestors() (TreeNode method) get_ascii() (TreeNode method) get_broken_branches() (NCBITaxa method) get_cached_content() (TreeNode method) get_children() (TreeNode method) get_closest_leaf() (TreeNode method) get_common_ancestor() (TreeNode method) get_common_names() (NCBITaxa method) get_descendant_by_node_id() (EvolNode method) get_descendant_evol_events() (PhyloNode method) get_descendant_taxa() (NCBITaxa 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_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_leaf_names() (TreeNode method) get_leaf_profiles() (ClusterNode method) get_leaves() (TreeNode method) get_leaves_by_name() (TreeNode method) get_lineage() (NCBITaxa 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_rank() (NCBITaxa method) get_seq() (SeqGroup method) get_silhouette() (ClusterNode method) get_sisters() (TreeNode method) get_speciation_trees() (PhyloNode method) get_species() (PhyloNode method) get_taxid_translator() (NCBITaxa method) get_topology() (NCBITaxa method) get_topology_id() (TreeNode 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

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_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)