Index

_

__init__() (BoxedFace method) (BoxFace method) (CircleFace method) (Decoration method) (EvalTextFace method) (Face method) (GTDBTaxa method) (ImageFace method) (Layout method) (LegendFace method) (NCBITaxa method) (PhyloTree method) (PolygonFace method) (PropFace method) (RectFace method) (SeqFace method) (SeqGroup method) (TextFace method) (Tree method) (TreePattern method)

A

add_branch_values() (in module ete4.core.operations) add_child() (Tree method) add_children() (Tree method) add_face() (Tree method) add_leaf_names() (in module ete4.core.operations) add_next_branch() (Walker method) add_prop() (Tree method) add_props() (Tree method) add_sister() (Tree method) add_tree() (in module ete4.smartview.explorer)

add_trees_from_request() (in module ete4.smartview.explorer) ancestors() (Tree method) anchor (Decoration attribute) (Label attribute) annotate_gtdb_taxa() (PhyloTree method) annotate_ncbi_taxa() (PhyloTree method) annotate_tree() (GTDBTaxa method) (NCBITaxa method) apply_translations() (in module ete4.parser.nexus) are_valid_angles() (in module ete4.smartview.graphics) assert_root_consistency() (in module ete4.core.operations)

B

Box (class in ete4.smartview.coordinates)

BoxedFace (class in ete4.smartview.faces) BoxFace (class in ete4.smartview.faces)

C

callback() (in module ete4.smartview.explorer) check_monophyly() (Tree method) children (Tree attribute) CircleFace (class in ete4.smartview.faces) code (Label attribute) collapse_lineage_specific_expansions() (PhyloTree method) column (Decoration attribute) (Label attribute)

common_ancestor() (in module ete4.core.operations) (Tree method) compare() (Tree method) content_repr() (in module ete4.parser.newick) cophenetic_matrix() (Tree method) copy() (Tree method) create_dichotomic_sister() (in module ete4.core.operations)

D

Decoration (class in ete4.smartview.layout) default_draw_node() (in module ete4.smartview.layout) del_prop() (Tree method) delete() (Tree method) descendants() (Tree method) describe() (Tree method) detach() (Tree method) dist (Tree attribute) draw() (BoxedFace method) (CircleFace method) (EvalTextFace method) (Face method) (PolygonFace method) (SeqFace method) draw_arc() (in module ete4.smartview.graphics) draw_array() (in module ete4.smartview.graphics) draw_box() (in module ete4.smartview.graphics) draw_circle() (in module ete4.smartview.graphics) draw_group() (in module ete4.smartview.graphics) draw_header() (in module ete4.smartview.graphics) draw_hz_line() (in module ete4.smartview.graphics)

draw_image() (in module ete4.smartview.graphics) draw_legend() (in module ete4.smartview.graphics) draw_line() (in module ete4.smartview.graphics) draw_node (Layout property) draw_nodebox() (in module ete4.smartview.graphics) draw_nodedot() (in module ete4.smartview.graphics) draw_outline() (in module ete4.smartview.graphics) draw_polygon() (in module ete4.smartview.graphics) draw_rect() (in module ete4.smartview.graphics) draw_seq() (in module ete4.smartview.graphics) draw_skeleton() (in module ete4.smartview.graphics) draw_text() (in module ete4.smartview.graphics) draw_texts() (in module ete4.smartview.faces) draw_tree (Layout property) draw_vt_line() (in module ete4.smartview.graphics) dump() (in module ete4.parser.newick) dumps() (in module ete4.parser.newick) dx (Box attribute) (Size attribute) dy (Box attribute) (Size attribute)

E

edges() (Tree method) error() (in module ete4.parser.newick) ete4.core.operations module ete4.core.seqgroup module ete4.parser.newick module ete4.parser.nexus module ete4.smartview.coordinates module ete4.smartview.explorer module

ete4.smartview.faces module ete4.smartview.graphics module ete4.smartview.layout module ete4.treematcher.treematcher module eval_as_str() (in module ete4.smartview.faces) EvalTextFace (class in ete4.smartview.faces) EvolEvent (class in ete4.phylo) expand_polytomies() (Tree method) explore() (in module ete4.smartview.explorer) (Tree method)

F

Face (class in ete4.smartview.faces) face (Decoration attribute) farthest() (in module ete4.core.operations) farthest_descendant() (in module ete4.core.operations)

first_value() (in module ete4.smartview.faces) first_visit (Walker property) from_parent_child_table() (Tree static method) from_skbio() (Tree static method) fs_max (Label attribute)

G

get_age() (PhyloTree method) get_age_balanced_outgroup() (PhyloTree method) get_broken_branches() (GTDBTaxa method) (NCBITaxa method) get_cached_content() (Tree method) get_children() (Tree method) get_closest_leaf() (Tree method) get_command_search() (in module ete4.smartview.explorer) get_commands() (in module ete4.parser.nexus) get_common_names() (GTDBTaxa method) (NCBITaxa method) get_descendant_evol_events() (PhyloTree method) get_descendant_taxa() (GTDBTaxa method) (NCBITaxa method) get_distance() (Tree method) get_drawing_kwargs() (in module ete4.smartview.explorer) get_entries() (SeqGroup method) get_eval_search() (in module ete4.smartview.explorer) get_extended_props() (in module ete4.parser.newick) get_farthest_leaf() (Tree method) get_farthest_node() (Tree method) get_farthest_oldest_leaf() (PhyloTree method) get_farthest_oldest_node() (PhyloTree method) get_fuzzy_name_translation() (NCBITaxa method) get_lineage() (NCBITaxa method) get_lineage_translator() (NCBITaxa method) get_midpoint_outgroup() (Tree method) get_monophyletic() (Tree method)

get_my_evol_events() (PhyloTree method) get_name_lineage() (GTDBTaxa method) get_name_translator() (NCBITaxa method) get_newick() (in module ete4.smartview.explorer) get_next_available_port() (in module ete4.smartview.explorer) get_prop() (Tree method) get_rank() (GTDBTaxa method) (NCBITaxa method) get_search_function() (in module ete4.smartview.explorer) get_section() (in module ete4.parser.nexus) get_sections() (in module ete4.parser.nexus) get_seq() (SeqGroup method) get_sisters() (Tree method) get_speciation_trees() (PhyloTree method) get_species() (PhyloTree method) get_taxid_translator() (NCBITaxa method) get_tid() (in module ete4.smartview.explorer) get_topological_search() (in module ete4.smartview.explorer) get_topology() (GTDBTaxa method) (NCBITaxa method) get_topology_id() (Tree method) get_trees() (in module ete4.parser.nexus) get_trees_from_file() (in module ete4.smartview.explorer) get_trees_from_form() (in module ete4.smartview.explorer) get_trees_from_nexus_or_newick() (in module ete4.smartview.explorer) get_xs() (in module ete4.smartview.coordinates) get_ys() (in module ete4.smartview.coordinates) go_back() (Walker method) GTDBTaxa (class in ete4)

H

has_unvisited_branches (Walker property)

I

id (Tree attribute) ImageFace (class in ete4.smartview.faces) img_style (Tree attribute) insert_intermediate() (in module ete4.core.operations) interchange_references() (in module ete4.core.operations)

is_leaf (Tree attribute) is_monophyletic() (Tree method) is_root (Tree attribute) iter_entries() (SeqGroup method) iter_prepostorder() (Tree method) iter_species() (PhyloTree method)

J

join_branch() (in module ete4.core.operations)

json_error() (in module ete4.smartview.explorer)

L

Label (class in ete4.smartview.layout) ladderize() (in module ete4.core.operations) (Tree method) Layout (class in ete4.smartview.layout) leaf_names() (Tree method) leaves() (Tree method) LegendFace (class in ete4.smartview.faces) level (Tree attribute)

lineage() (Tree method) link_to_alignment() (PhyloTree method) load() (in module ete4.parser.newick) (in module ete4.parser.nexus) load_tree() (in module ete4.smartview.explorer) loads() (in module ete4.parser.newick) (in module ete4.parser.nexus) (in module ete4.smartview.explorer)

M

make_box() (in module ete4.smartview.coordinates) make_name() (in module ete4.core.operations) (in module ete4.smartview.explorer) make_nodes_summary() (in module ete4.smartview.faces) make_parser() (in module ete4.parser.newick) match() (in module ete4.treematcher.treematcher) (TreePattern method) midpoint() (in module ete4.core.operations) module ete4.core.operations ete4.core.seqgroup ete4.parser.newick ete4.parser.nexus ete4.smartview.coordinates ete4.smartview.explorer ete4.smartview.faces ete4.smartview.graphics ete4.smartview.layout ete4.treematcher.treematcher treeview

move() (in module ete4.core.operations)

N

name (Tree attribute) ncbi_compare() (PhyloTree method) NCBITaxa (class in ete4) NewickError

NexusError nice_html() (in module ete4.smartview.explorer) node (Walker property) node_id (Walker property) node_type (Label attribute)

O

open_browser_window() (in module ete4.smartview.explorer)

P

PhyloTree (class in ete4) PolygonFace (class in ete4.smartview.faces) pop_child() (Tree method) populate() (in module ete4.core.operations) (Tree method) populate_uniform() (in module ete4.core.operations)

populate_yule() (in module ete4.core.operations) position (Decoration attribute) (Label attribute) prop_repr() (in module ete4.parser.newick) PropFace (class in ete4.smartview.faces) props (Tree attribute) prune() (Tree method)

Q

quote() (in module ete4.parser.newick)

R

read_content() (in module ete4.parser.newick) read_node() (in module ete4.parser.newick) read_nodes() (in module ete4.parser.newick) read_props() (in module ete4.parser.newick) reconcile() (PhyloTree method) RectFace (class in ete4.smartview.faces) rehang() (in module ete4.core.operations) remove() (in module ete4.core.operations) remove_child() (Tree method) remove_children() (Tree method) remove_sister() (Tree method)

remove_tree() (in module ete4.smartview.explorer) render() (Tree method) render_sm() (Tree method) repr_short() (in module ete4.parser.newick) req_json() (in module ete4.smartview.explorer) resolve_polytomy() (in module ete4.core.operations) (Tree method) reverse_children() (Tree method) robinson_foulds() (Tree method) root (Tree attribute) root_at() (in module ete4.core.operations)

S

safer_eval() (in module ete4.smartview.explorer) (in module ete4.smartview.faces) (in module ete4.treematcher.treematcher) search() (in module ete4.treematcher.treematcher) (TreePattern method) search_ancestors() (Tree method) search_descendants() (Tree method) search_leaves_by_name() (Tree method) search_nodes() (Tree method) SeqFace (class in ete4.smartview.faces) SeqGroup (class in ete4.core.seqgroup) set_midpoint_outgroup() (in module ete4.core.operations) set_outgroup() (in module ete4.core.operations) (Tree method) set_panel() (in module ete4.smartview.graphics) set_seq() (SeqGroup method) set_species_naming_function() (PhyloTree method) set_style() (Tree method) set_xmaxs() (in module ete4.smartview.graphics)

show() (Tree method) Size (class in ete4.smartview.coordinates) size (Tree attribute) skip_content() (in module ete4.parser.newick) skip_quoted_name() (in module ete4.parser.newick) skip_spaces_and_comments() (in module ete4.parser.newick) sort() (in module ete4.core.operations) (in module ete4.smartview.explorer) sort_descendants() (Tree method) species (PhyloTree property) split_by_dups() (PhyloTree method) standardize() (Tree method) start_server() (in module ete4.smartview.explorer) stop_server() (in module ete4.smartview.explorer) store_search() (in module ete4.smartview.explorer) style (Label attribute) support (Tree attribute) swap_children() (Tree method) swap_props() (in module ete4.core.operations)

T

text_repr() (in module ete4.smartview.faces) TextFace (class in ete4.smartview.faces) texts_size() (in module ete4.smartview.faces) to_dendrogram() (in module ete4.core.operations) to_elements() (in module ete4.smartview.layout) to_str() (Tree method) to_ultrametric() (in module ete4.core.operations) (Tree method)

translate_to_names() (NCBITaxa method) traverse() (in module ete4.core.operations) (Tree method) traverse_bfs() (in module ete4.core.operations) Tree (class in ete4) TreePattern (class in ete4.treematcher.treematcher) treeview module

U

unquote() (in module ete4.parser.newick) unroot() (in module ete4.core.operations) (Tree method) up (Tree attribute) update_size() (in module ete4.core.operations)

update_sizes_all() (in module ete4.core.operations) update_sizes_from() (in module ete4.core.operations) update_style() (in module ete4.smartview.layout) update_taxonomy_database() (GTDBTaxa method) (NCBITaxa method)

W

walk() (in module ete4.core.operations) Walker (class in ete4.core.operations)

write() (PhyloTree method) (SeqGroup method) (Tree method)

X

x (Box attribute)

Y

y (Box attribute)