Index

_

__init__() (AlignedGrid method) (AlignLinkFace method) (AlignmentFace method) (ArrowFace method) (AttrFace method) (CircleFace method) (ClusterTree method) (Drawer method) (DrawerCirc method) (Face method) (GTDBTaxa method) (HTMLFace method) (ImgFace method) (LayoutAlignment method) (LayoutAutoName method) (LayoutBarplot method) (LayoutBestName method) (LayoutBigg method) (LayoutBranchLength method) (LayoutBranchSupport method) (LayoutCard method) (LayoutCazy method) (LayoutCuratedName method) (LayoutEteDiffDistance method) (LayoutEukOgs method) (LayoutEvolEvents method), [1] (LayoutGenomicContext method) (LayoutHumanOGs method) (LayoutKeggEnzyme method) (LayoutKeggModule method) (LayoutKeggNumber method) (LayoutKeggPathway method) (LayoutLastCommonAncestor method), [1] (LayoutLeafName method) (LayoutNumberLeaves method) (LayoutOutline method) (LayoutPdb method) (LayoutPfamDomains method), [1] (LayoutPreferredName method) (LayoutProteinName method) (LayoutScientificName method) (LayoutSciName method) (LayoutSeeds method) (LayoutSmartDomains method), [1] (LayoutUCSC method) (LayoutUCSCtrans method) (LegendFace method) (NCBITaxa method) (NodeStyle method) (OutlineFace method) (PhyloTree method) (PieChartFace method) (RectFace method) (ScaleFace method) (SelectedCircleFace method) (SelectedFace method) (SelectedRectFace method) (SeqFace method) (SeqGroup method) (SeqMotifFace method) (StackedBarFace method) (TextFace method) (Tree method) (TreeData method) (TreeLayout method) (TreePattern method) (TreeStyle method)

A

activate_clade() (in module ete4.smartview.gui.server) activate_node() (in module ete4.smartview.gui.server) Active (class in ete4.smartview.renderer.drawer) active (TreeData attribute) active_face (TreeStyle property) active_face_pos (TreeStyle property) add_branch_values() (in module ete4.core.operations) add_child() (Tree method) add_children() (Tree method) add_face() (Grid method) (Tree method) add_face_smartview() (Tree method) add_face_treeview() (Tree method) add_feature() (Tree method) add_features() (Tree method) add_leaf_names() (in module ete4.core.operations) add_legend() (TreeStyle method) add_next_branch() (Walker method)

add_prop() (Tree method) add_props() (Tree method) add_sister() (Tree method) add_tree() (in module ete4.smartview.gui.server) add_trees_from_request() (in module ete4.smartview.gui.server) aligned_panel_footer (TreeStyle property) aligned_panel_header (TreeStyle property) AlignedGrid (class in ete4.smartview.renderer.face_positions) AlignLinkFace (class in ete4.smartview.renderer.faces) AlignmentFace (class in ete4.smartview.renderer.faces) ancestors() (Tree method) annotate_gtdb_taxa() (PhyloTree method) annotate_ncbi_taxa() (PhyloTree method) annotate_tree() (GTDBTaxa method) (NCBITaxa method) apply_translations() (in module ete4.parser.nexus) ArrowFace (class in ete4.smartview.renderer.faces) assert_root_consistency() (in module ete4.core.operations) AttrFace (class in ete4.smartview.renderer.faces)

B

Box (class in ete4.smartview.renderer.draw_helpers)

build_blocks() (AlignmentFace method) build_regions() (SeqMotifFace method)

C

callback() (in module ete4.smartview.gui.server) cartesian() (in module ete4.smartview.renderer.draw_helpers) cased_name() (in module ete4.smartview.renderer.treelayout) change_selection_name() (in module ete4.smartview.gui.server) check_monophyly() (Tree method) children (Tree attribute) CircleFace (class in ete4.smartview.renderer.faces) circumasec() (in module ete4.smartview.renderer.draw_helpers) circumrect() (in module ete4.smartview.renderer.draw_helpers) clades (TreeActive attribute) clip_angles() (in module ete4.smartview.renderer.draw_helpers) ClusterTree (class in ete4.clustering.clustertree) collapse_lineage_specific_expansions() (PhyloTree method) COLLAPSE_SIZE (Drawer attribute) collapsed_faces (Tree attribute) common_ancestor() (in module ete4.core.operations) (Tree method) compare() (Tree method)

compute_bounding_box() (AlignLinkFace method) (AlignmentFace method) (CircleFace method) (Face method) (OutlineFace method) (RectFace method) (ScaleFace method) (SeqFace method) (SeqMotifFace method) (TextFace method) compute_fsize() (Face method) compute_pie() (PieChartFace method) content_repr() (in module ete4.parser.newick) content_size() (DrawerCirc method) (DrawerRect method) cophenetic_matrix() (Tree method) copy() (Tree method) copy_style() (in module ete4.smartview.gui.server) create_dichotomic_sister() (in module ete4.core.operations)

D

deactivate_clade() (in module ete4.smartview.gui.server) deactivate_node() (in module ete4.smartview.gui.server) del_feature() (Tree method) del_prop() (Tree method) del_tree() (in module ete4.smartview.gui.server) delete() (Tree method) descendants() (Tree method) describe() (Tree method) detach() (Tree method) deviation (ClusterTree property) dist (Tree attribute) dist() (in module ete4.smartview.renderer.drawer) draw() (AlignLinkFace method) (AlignmentFace method) (ArrowFace method) (CircleFace method) (Drawer method) (HTMLFace method) (ImgFace method) (LegendFace method) (OutlineFace method) (PieChartFace method) (RectFace method) (ScaleFace method) (SeqFace method) (SeqMotifFace method) (StackedBarFace method) (TextFace method) draw_aligned_headers() (Drawer method) draw_arc() (in module ete4.smartview.renderer.draw_helpers) draw_array() (in module ete4.smartview.renderer.draw_helpers) draw_arrow() (in module ete4.smartview.renderer.draw_helpers) draw_childrenline() (DrawerCirc method) (DrawerRect method) draw_circle() (in module ete4.smartview.renderer.draw_helpers) draw_collapsed() (Drawer method) (DrawerCirc method) (DrawerCircFaces method) (DrawerRect method) (DrawerRectFaces method)

draw_content() (Drawer method) draw_ellipse() (in module ete4.smartview.renderer.draw_helpers) draw_html() (in module ete4.smartview.renderer.draw_helpers) draw_img() (in module ete4.smartview.renderer.draw_helpers) draw_lengthline() (DrawerCirc method) (DrawerRect method) draw_line() (in module ete4.smartview.renderer.draw_helpers) draw_node() (Drawer method) (DrawerCircFaces method) (DrawerRectFaces method) draw_nodebox() (DrawerCirc method) (DrawerRect method) (in module ete4.smartview.renderer.draw_helpers) draw_nodedot() (DrawerCirc method) (DrawerRect method) draw_outline() (in module ete4.smartview.renderer.draw_helpers) draw_rect() (in module ete4.smartview.renderer.draw_helpers) draw_rhombus() (in module ete4.smartview.renderer.draw_helpers) draw_slice() (in module ete4.smartview.renderer.draw_helpers) draw_text() (in module ete4.smartview.renderer.draw_helpers) draw_triangle() (in module ete4.smartview.renderer.draw_helpers) Drawer (class in ete4.smartview.renderer.drawer) DrawerAlignCircFaces (class in ete4.smartview.renderer.drawer) DrawerAlignRectFaces (class in ete4.smartview.renderer.drawer) DrawerCirc (class in ete4.smartview.renderer.drawer) DrawerCircFaces (class in ete4.smartview.renderer.drawer) DrawerRect (class in ete4.smartview.renderer.drawer) DrawerRectFaces (class in ete4.smartview.renderer.drawer) drawn_size() (in module ete4.smartview.renderer.drawer) 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.clustering.clustertree module ete4.core.operations module ete4.core.seqgroup module ete4.parser.newick module ete4.parser.nexus module ete4.smartview.gui.server module ete4.smartview.renderer.draw_helpers module ete4.smartview.renderer.drawer module ete4.smartview.renderer.face_positions module ete4.smartview.renderer.faces module ete4.smartview.renderer.layouts.context_layouts module ete4.smartview.renderer.layouts.default_layouts module ete4.smartview.renderer.layouts.domain_layouts module ete4.smartview.renderer.layouts.eggnog6_layouts module

ete4.smartview.renderer.layouts.etecompare_layouts module ete4.smartview.renderer.layouts.evocell_layouts module ete4.smartview.renderer.layouts.evol_events_layouts module ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts module ete4.smartview.renderer.layouts.seq_layouts module ete4.smartview.renderer.layouts.spongilla_layouts module ete4.smartview.renderer.layouts.staple_layouts module ete4.smartview.renderer.nodestyle module ete4.smartview.renderer.treelayout module ete4.smartview.renderer.treestyle module ete4.treematcher.treematcher module EvolEvent (class in ete4.phylo) exclude_props (TreeData attribute) expand_polytomies() (Tree method) explore() (Tree method)

F

Face (class in ete4.smartview.renderer.faces) faces (Tree attribute) farthest() (in module ete4.core.operations) farthest_descendant() (in module ete4.core.operations) find_node() (in module ete4.smartview.gui.server) first_value() (in module ete4.smartview.renderer.draw_helpers) first_visit (Walker property) fits() (AlignLinkFace method) (Face method) (OutlineFace method) (SeqMotifFace method) (TextFace method)

flush_outline() (Drawer method) (DrawerCirc method) from_parent_child_table() (Tree static method) from_skbio() (Tree static method)

G

get_active_children() (Drawer method) get_active_clade() (in module ete4.smartview.gui.server) get_active_clades() (in module ete4.smartview.gui.server) get_age() (PhyloTree method) get_age_balanced_outgroup() (PhyloTree method) get_asec() (in module ete4.smartview.renderer.drawer) get_box() (AlignLinkFace method) (DrawerCirc method) (DrawerRect method) (Face method) (OutlineFace method) get_broken_branches() (GTDBTaxa method) (NCBITaxa method) get_cached_content() (Tree method) get_children() (Tree method) get_closest_leaf() (Tree method) get_collapsed_node() (Drawer method) get_color() (LayoutLastCommonAncestor method), [1] get_command_search() (in module ete4.smartview.gui.server) get_commands() (in module ete4.parser.nexus) get_common_names() (GTDBTaxa method) (NCBITaxa method) get_content() (AttrFace method) (Face method) get_context() (LayoutGenomicContext method) get_descendant_evol_events() (PhyloTree method) get_descendant_taxa() (GTDBTaxa method) (NCBITaxa method) get_distance() (Tree method) get_drawer() (in module ete4.smartview.gui.server) get_drawers() (in module ete4.smartview.renderer.drawer) get_dunn() (ClusterTree method) get_empty_active() (in module ete4.smartview.renderer.drawer) get_entries() (SeqGroup method) get_eval_search() (in module ete4.smartview.gui.server) 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_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts) get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts) get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts) get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts) get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts) get_layouts() (in module ete4.smartview.gui.server) get_layouts_from_getters() (in module ete4.smartview.gui.server) get_legend() (TreeStyle method) get_line_type() (in module ete4.smartview.renderer.draw_helpers)

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.gui.server) get_next_available_port() (in module ete4.smartview.gui.server) get_nodes_info() (in module ete4.smartview.gui.server) get_outline() (Drawer method) get_parents() (in module ete4.smartview.gui.server) get_parser() (in module ete4.smartview.gui.server) get_popup_props() (Drawer method) get_prop() (Tree method) get_props() (in module ete4.parser.newick) get_rank() (GTDBTaxa method) (NCBITaxa method) get_rect() (in module ete4.smartview.renderer.drawer) get_search_function() (in module ete4.smartview.gui.server) get_section() (in module ete4.parser.nexus) get_sections() (in module ete4.parser.nexus) get_selected_children() (Drawer method) get_selection_info() (in module ete4.smartview.gui.server) get_selections() (in module ete4.smartview.gui.server) get_seq() (AlignmentFace method) (LayoutAlignment method) (SeqGroup method) get_silhouette() (ClusterTree method) get_sisters() (Tree method) get_speciation_trees() (PhyloTree method) get_species() (PhyloTree method) get_stats() (in module ete4.smartview.gui.server) get_taxid_translator() (NCBITaxa method) get_tid() (in module ete4.smartview.gui.server) get_tooltip() (LayoutGenomicContext method) get_topological_search() (in module ete4.smartview.gui.server) 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.gui.server) get_trees_from_form() (in module ete4.smartview.gui.server) get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server) get_xs() (in module ete4.smartview.renderer.draw_helpers) get_ys() (in module ete4.smartview.renderer.draw_helpers) GlobalStuff (class in ete4.smartview.gui.server) go_back() (Walker method) Grid (class in ete4.smartview.renderer.face_positions) GTDBTaxa (class in ete4)

H

has_unvisited_branches (Walker property)

HTMLFace (class in ete4.smartview.renderer.faces)

I

id (Tree attribute) img_style (Tree property) ImgFace (class in ete4.smartview.renderer.faces) in_aligned_viewport() (Face method) in_viewport() (DrawerCirc method) (DrawerRect method) include_props (TreeData attribute) init() (NodeStyle method) init_from_ete() (Tree method) init_from_newick() (Tree method) initialize() (in module ete4.smartview.gui.server) initialize_tree_style() (in module ete4.smartview.gui.server) initialized (TreeData attribute) insert_intermediate() (in module ete4.core.operations) interchange_references() (in module ete4.core.operations)

intercluster_dist (ClusterTree property) intersects_angles() (in module ete4.smartview.renderer.draw_helpers) intersects_box() (in module ete4.smartview.renderer.draw_helpers) intersects_segment() (in module ete4.smartview.renderer.draw_helpers) intracluster_dist (ClusterTree property) is_collapsed (Tree property) is_fully_collapsed() (Drawer method) is_initialized (Tree property) is_leaf (Tree attribute) is_monophyletic() (Tree method) is_root (Tree attribute) is_small() (DrawerCirc method) (DrawerRect method) 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.gui.server)

L

ladderize() (in module ete4.core.operations) (Tree method) LayoutAlignment (class in ete4.smartview.renderer.layouts.seq_layouts) LayoutAutoName (class in ete4.smartview.renderer.layouts.spongilla_layouts) LayoutBarplot (class in ete4.smartview.renderer.layouts.staple_layouts) LayoutBestName (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutBigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutBranchLength (class in ete4.smartview.renderer.layouts.default_layouts) LayoutBranchSupport (class in ete4.smartview.renderer.layouts.default_layouts) LayoutCard (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutCazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutCuratedName (class in ete4.smartview.renderer.layouts.spongilla_layouts) LayoutEteDiffDistance (class in ete4.smartview.renderer.layouts.etecompare_layouts) LayoutEukOgs (class in ete4.smartview.renderer.layouts.spongilla_layouts) LayoutEvolEvents (class in ete4.smartview.renderer.layouts.eggnog6_layouts) (class in ete4.smartview.renderer.layouts.evol_events_layouts) LayoutGenomicContext (class in ete4.smartview.renderer.layouts.context_layouts) LayoutHumanOGs (class in ete4.smartview.renderer.layouts.evocell_layouts) LayoutKeggEnzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutKeggModule (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutKeggNumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutKeggPathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutLastCommonAncestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts) (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts) LayoutLeafName (class in ete4.smartview.renderer.layouts.default_layouts) LayoutNumberLeaves (class in ete4.smartview.renderer.layouts.default_layouts) LayoutOutline (class in ete4.smartview.renderer.layouts.default_layouts)

LayoutPdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutPfamDomains (class in ete4.smartview.renderer.layouts.domain_layouts) (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutPreferredName (class in ete4.smartview.renderer.layouts.spongilla_layouts) LayoutProteinName (class in ete4.smartview.renderer.layouts.eggnog6_layouts) layouts (TreeData attribute) LayoutScientificName (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutSciName (class in ete4.smartview.renderer.layouts.spongilla_layouts) LayoutSeeds (class in ete4.smartview.renderer.layouts.spongilla_layouts) LayoutSmartDomains (class in ete4.smartview.renderer.layouts.domain_layouts) (class in ete4.smartview.renderer.layouts.eggnog6_layouts) LayoutUCSC (class in ete4.smartview.renderer.layouts.evocell_layouts) LayoutUCSCtrans (class in ete4.smartview.renderer.layouts.evocell_layouts) leaf_names() (Tree method) leaf_profiles() (ClusterTree method) leaves() (Tree method) LegendFace (class in ete4.smartview.renderer.faces) level (Tree attribute) lineage() (Tree method) link_to_alignment() (PhyloTree method) link_to_arraytable() (ClusterTree method) load() (in module ete4.parser.newick) (in module ete4.parser.nexus) load_tree() (in module ete4.smartview.gui.server) load_tree_from_newick() (in module ete4.smartview.gui.server) loads() (in module ete4.parser.newick) (in module ete4.parser.nexus)

M

maintenance() (in module ete4.smartview.gui.server) make_box() (in module ete4.smartview.renderer.drawer) make_faces() (in module ete4.smartview.renderer.face_positions) make_name() (in module ete4.core.operations) (in module ete4.smartview.gui.server) make_parser() (in module ete4.parser.newick) match() (in module ete4.treematcher.treematcher) (TreePattern method) midpoint() (in module ete4.core.operations) MIN_SIZE (Drawer attribute) module ete4.clustering.clustertree ete4.core.operations ete4.core.seqgroup ete4.parser.newick ete4.parser.nexus ete4.smartview.gui.server ete4.smartview.renderer.draw_helpers ete4.smartview.renderer.drawer ete4.smartview.renderer.face_positions ete4.smartview.renderer.faces ete4.smartview.renderer.layouts.context_layouts ete4.smartview.renderer.layouts.default_layouts ete4.smartview.renderer.layouts.domain_layouts ete4.smartview.renderer.layouts.eggnog6_layouts ete4.smartview.renderer.layouts.etecompare_layouts ete4.smartview.renderer.layouts.evocell_layouts ete4.smartview.renderer.layouts.evol_events_layouts ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts ete4.smartview.renderer.layouts.phylocloud_egg5_layouts ete4.smartview.renderer.layouts.seq_layouts ete4.smartview.renderer.layouts.spongilla_layouts ete4.smartview.renderer.layouts.staple_layouts ete4.smartview.renderer.nodestyle ete4.smartview.renderer.treelayout ete4.smartview.renderer.treestyle ete4.treematcher.treematcher treeview

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

N

name (Tree attribute) (TreeData attribute) ncbi_compare() (PhyloTree method) NCBITaxa (class in ete4) NewickError NexusError nice_html() (in module ete4.smartview.gui.server) node (Walker property)

node_id (Walker property) node_size() (DrawerCirc method) (DrawerRect method) nodes (TreeActive attribute) NodeStyle (class in ete4.smartview.renderer.nodestyle) nodestyles (TreeData attribute) NPANELS (Drawer attribute) (DrawerAlignCircFaces attribute) (DrawerAlignRectFaces attribute)

O

on_first_visit() (Drawer method) on_last_visit() (Drawer method)

open_browser_window() (in module ete4.smartview.gui.server) orientation (ArrowFace property) OutlineFace (class in ete4.smartview.renderer.faces)

P

Padding (class in ete4.smartview.renderer.draw_helpers) parents (Active attribute) PhyloTree (class in ete4) PieChartFace (class in ete4.smartview.renderer.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) profile (ClusterTree property) prop_repr() (in module ete4.parser.newick) props (Tree attribute) prune() (Tree method) prune_by_selection() (in module ete4.smartview.gui.server)

Q

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

R

read_content() (in module ete4.parser.newick) read_nodes() (in module ete4.parser.newick) reconcile() (PhyloTree method) RectFace (class in ete4.smartview.renderer.faces) rehang() (in module ete4.core.operations) remove() (in module ete4.core.operations) remove_active() (in module ete4.smartview.gui.server) remove_active_clade() (in module ete4.smartview.gui.server) remove_child() (Tree method) remove_children() (Tree method) remove_search() (in module ete4.smartview.gui.server) remove_selection() (in module ete4.smartview.gui.server) remove_sister() (Tree method)

render() (Tree method) repr_short() (in module ete4.parser.newick) req_json() (in module ete4.smartview.gui.server) resolve_polytomy() (in module ete4.core.operations) (Tree method) results (Active attribute) retrieve_layouts() (in module ete4.smartview.gui.server) retrieve_tree_data() (in module ete4.smartview.gui.server) reverse_children() (Tree method) robinson_foulds() (Tree method) root (Tree attribute) root_at() (in module ete4.core.operations) run_smartview() (in module ete4.smartview.gui.server)

S

safe_string() (in module ete4.smartview.renderer.drawer) safer_eval() (in module ete4.smartview.gui.server) (in module ete4.treematcher.treematcher) ScaleFace (class in ete4.smartview.renderer.faces) 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) search_to_selection() (in module ete4.smartview.gui.server) searches (TreeData attribute) selected (TreeData attribute) selected_face (TreeStyle property) selected_face_pos (TreeStyle property) SelectedCircleFace (class in ete4.smartview.renderer.faces) SelectedFace (class in ete4.smartview.renderer.faces) SelectedRectFace (class in ete4.smartview.renderer.faces) SeqFace (class in ete4.smartview.renderer.faces) SeqGroup (class in ete4.core.seqgroup) SeqMotifFace (class in ete4.smartview.renderer.faces) set_distance_function() (ClusterTree method) set_midpoint_outgroup() (in module ete4.core.operations) set_node_style() (LayoutAlignment method) (LayoutAutoName method) (LayoutBarplot method) (LayoutCuratedName method) (LayoutEteDiffDistance method) (LayoutEukOgs method) (LayoutEvolEvents method), [1] (LayoutGenomicContext method) (LayoutHumanOGs method) (LayoutLastCommonAncestor method), [1] (LayoutLeafName method) (LayoutNumberLeaves method) (LayoutOutline method) (LayoutPreferredName method) (LayoutSciName method) (LayoutSeeds method) (LayoutUCSC method) (LayoutUCSCtrans method) (TreeLayout method)

set_outgroup() (in module ete4.core.operations) (Tree method) set_seq() (SeqGroup method) set_species_naming_function() (PhyloTree method) set_style() (Tree method) set_tree_style() (LayoutAlignment method) (LayoutBarplot method) (LayoutEvolEvents method), [1] (LayoutGenomicContext method) (TreeLayout method) show() (Tree method) silhouette (ClusterTree property) Size (class in ete4.smartview.renderer.drawer) size (Tree attribute) skip_quoted_name() (in module ete4.parser.newick) skip_spaces_and_comments() (in module ete4.parser.newick) sm_style (Tree property) sort() (in module ete4.core.operations) (in module ete4.smartview.gui.server) sort_descendants() (Tree method) species (PhyloTree property) split_by_dups() (PhyloTree method) split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers) stack() (in module ete4.smartview.renderer.drawer) StackedBarFace (class in ete4.smartview.renderer.faces) standardize() (Tree method) store_active() (in module ete4.smartview.gui.server) store_search() (in module ete4.smartview.gui.server) store_selection() (in module ete4.smartview.gui.server) style (TreeData attribute) summary() (in module ete4.smartview.renderer.draw_helpers) support (Tree attribute) swap_children() (Tree method) swap_props() (in module ete4.core.operations)

T

TextFace (class in ete4.smartview.renderer.faces) timer (TreeData attribute) to_dendrogram() (in module ete4.core.operations) to_str() (Tree method) to_ultrametric() (in module ete4.core.operations) (Tree method) touch_and_get() (in module ete4.smartview.gui.server) translate_to_names() (NCBITaxa method) traverse() (in module ete4.core.operations) (Tree method) traverse_bfs() (in module ete4.core.operations)

Tree (class in ete4) tree (TreeData attribute) TreeActive (class in ete4.smartview.renderer.drawer) TreeData (class in ete4.smartview.gui.server) TreeLayout (class in ete4.smartview.renderer.treelayout) TreePattern (class in ete4.treematcher.treematcher) TreeStyle (class in ete4.smartview.renderer.treestyle) treeview module TYPE (Drawer attribute) (DrawerCirc attribute) (DrawerRect attribute)

U

ultrametric (TreeData attribute) unquote() (in module ete4.parser.newick) unroot() (in module ete4.core.operations) (Tree method) unselect_node() (in module ete4.smartview.gui.server) up (Tree attribute) update_app_available_layouts() (in module ete4.smartview.gui.server) update_layouts() (in module ete4.smartview.gui.server)

update_node_props() (in module ete4.smartview.gui.server) update_node_style() (in module ete4.smartview.gui.server) update_selection() (in module ete4.smartview.gui.server) update_size() (in module ete4.core.operations) update_sizes_all() (in module ete4.core.operations) update_sizes_from() (in module ete4.core.operations) 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) (Padding attribute)

Y

y (Box attribute) (Padding attribute)