integer number representing the width
-of the line in pixels. A line width of zero indicates a +
draw_descendants (True) – Mark an internal node as a leaf.
hz_line_width (0) – integer number representing the width +of the line in pixels. A line width of zero indicates a cosmetic pen. This means that the pen width is always drawn one pixel wide, independent of the transformation -set on the painter.
-vt_line_width (0) – integer number representing the width of the line in pixels. A line width of zero indicates a cosmetic pen. 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"frequently-asked-questions-faqs"]], "Contents": [[1, "contents"], [9, "contents"], [11, "contents"], [13, "contents"], [14, "contents"]], "General": [[1, "general"]], "How do I use ETE?": [[1, "how-do-i-use-ete"]], "Tree Browsing": [[1, "tree-browsing"]], "How do I find a leaf by its name?": [[1, "how-do-i-find-a-leaf-by-its-name"]], "How do I visit all nodes within a tree?": [[1, "how-do-i-visit-all-nodes-within-a-tree"]], "Can I control the order in which nodes are visited?": [[1, "can-i-control-the-order-in-which-nodes-are-visited"]], "Reading and writing": [[1, "reading-and-writing"]], "How do I load a tree with internal node names or support?": [[1, "how-do-i-load-a-tree-with-internal-node-names-or-support"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "Tree visualization": [[1, "tree-visualization"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "Can the visualization of trees with very unbalanced tree branches be improved?": [[1, "can-the-visualization-of-trees-with-very-unbalanced-tree-branches-be-improved"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Contents:": [[2, null]], "Indices and tables": [[2, "indices-and-tables"]], "Reference Guide": [[3, "reference-guide"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "NCBITaxa": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "Tree operations": [[6, "module-ete4.core.operations"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [13, "phylogenetic-trees"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Renderer": [[9, "renderer"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [11, "faces"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "Nexus": [[9, "nexus"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [11, "nodestyle"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [11, "treestyle"]], "Layouts": [[9, "layouts"]], "context": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Tree (main class)": [[10, "tree-main-class"]], "Treeview (qt graphics)": [[11, "treeview-qt-graphics"]], "ETE Tutorial": [[12, "ete-tutorial"]], "Overview": [[13, "overview"]], "Linking phylogenetic trees with multiple sequence alignments": [[13, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[13, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[13, "adding-taxonomic-information"]], "Automatic control of species info": [[13, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[13, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[13, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[13, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[13, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[13, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[13, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[13, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[13, "implementation"]], "Automatic rooting (outgroup detection)": [[13, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[13, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[13, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[13, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[13, "collapse-species-specific-duplications"]], "Working with the Tree structure": [[14, "working-with-the-tree-structure"]], "Trees": [[14, "trees"]], "Reading and writing newick trees": [[14, "reading-and-writing-newick-trees"]], "Creating a tree": [[14, "creating-a-tree"]], "Reading newick trees": [[14, "reading-newick-trees"]], "Writing newick trees": [[14, "writing-newick-trees"]], "Understanding ETE trees": [[14, "understanding-ete-trees"]], "Basic tree attributes": [[14, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[14, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[14, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[14, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[14, "traversing-browsing-trees"]], "Advanced traversing": [[14, "advanced-traversing"]], "Collapsing nodes while traversing": [[14, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[14, "iterators-or-lists"]], "Finding nodes by their properties": [[14, "finding-nodes-by-their-properties"]], "Search_all nodes matching a given criteria": [[14, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria (iteration)": [[14, "search-nodes-matching-a-given-criteria-iteration"]], "Find the first common ancestor": [[14, "find-the-first-common-ancestor"]], "Custom searching functions": [[14, "custom-searching-functions"]], "Shortcuts": [[14, "shortcuts"]], "Checking the monophyly of properties within a tree": [[14, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[14, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[14, "node-annotation"]], "Comparing trees": [[14, "comparing-trees"]], "Distances between trees": [[14, "distances-between-trees"]], "Robinson-Foulds distance": [[14, "robinson-foulds-distance"]], "Modifying tree topology": [[14, "modifying-tree-topology"]], "Creating trees from scratch": [[14, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[14, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[14, "pruning-trees"]], "Concatenating trees": [[14, "concatenating-trees"]], "Copying (duplicating) trees": [[14, "copying-duplicating-trees"]], "Solving multifurcations": [[14, "solving-multifurcations"]], "Tree rooting": [[14, "tree-rooting"]], "Working with branch distances": [[14, "working-with-branch-distances"]], "Getting distances between nodes": [[14, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[14, "getting-midpoint-outgroup"]]}, "indexentries": {"clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree"]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__"]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation"]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree"]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn"]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette"]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist"]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist"]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles"]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable"]], "module": [[4, "module-ete4.clustering.clustertree"], [5, "module-ete4.ncbi_taxonomy.ncbiquery"], [6, "module-ete4.core.operations"], [8, "module-ete4.core.seqgroup"], [9, "module-ete4.smartview.gui.server"], [9, "module-ete4.smartview.renderer.draw_helpers"], [9, "module-ete4.smartview.renderer.drawer"], [9, "module-ete4.smartview.renderer.face_positions"], [9, "module-ete4.smartview.renderer.faces"], [9, "module-ete4.smartview.renderer.layouts.context_layouts"], [9, "module-ete4.smartview.renderer.layouts.default_layouts"], [9, "module-ete4.smartview.renderer.layouts.domain_layouts"], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [9, "module-ete4.smartview.renderer.layouts.seq_layouts"], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [9, "module-ete4.smartview.renderer.layouts.staple_layouts"], [9, "module-ete4.smartview.renderer.nodestyle"], [9, "module-ete4.smartview.renderer.treelayout"], [9, "module-ete4.smartview.renderer.treestyle"]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile"]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function"]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette"]], "ncbitaxa (class in ete4.ncbi_taxonomy.ncbiquery)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa"]], "__init__() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.__init__"]], "annotate_tree() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.annotate_tree"]], "ete4.ncbi_taxonomy.ncbiquery": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "get_broken_branches() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_broken_branches"]], "get_common_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_common_names"]], "get_descendant_taxa() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage"]], "get_lineage_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage_translator"]], "get_name_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_name_translator"]], "get_rank() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_rank"]], "get_taxid_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_taxid_translator"]], "get_topology() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_topology"]], "is_taxadb_up_to_date() (in module ete4.ncbi_taxonomy.ncbiquery)": [[5, "ete4.ncbi_taxonomy.ncbiquery.is_taxadb_up_to_date"]], "translate_to_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.update_taxonomy_database"]], "walker (class in ete4.core.operations)": [[6, "ete4.core.operations.Walker"]], "add_next_branch() (walker method)": [[6, "ete4.core.operations.Walker.add_next_branch"]], "assert_root_consistency() (in module ete4.core.operations)": [[6, "ete4.core.operations.assert_root_consistency"]], "common_ancestor() (in module ete4.core.operations)": [[6, "ete4.core.operations.common_ancestor"]], "ete4.core.operations": [[6, "module-ete4.core.operations"]], "first_visit (walker property)": [[6, "ete4.core.operations.Walker.first_visit"]], "go_back() (walker method)": [[6, "ete4.core.operations.Walker.go_back"]], "has_unvisited_branches (walker property)": [[6, "ete4.core.operations.Walker.has_unvisited_branches"]], "insert_intermediate() (in module ete4.core.operations)": [[6, "ete4.core.operations.insert_intermediate"]], "join_branch() (in module ete4.core.operations)": [[6, "ete4.core.operations.join_branch"]], "ladderize() (in module ete4.core.operations)": [[6, "ete4.core.operations.ladderize"]], "maybe_convert_internal_nodes_to_support() (in module ete4.core.operations)": [[6, "ete4.core.operations.maybe_convert_internal_nodes_to_support"]], "move() (in module ete4.core.operations)": [[6, "ete4.core.operations.move"]], "node (walker property)": [[6, "ete4.core.operations.Walker.node"]], "node_id (walker property)": [[6, "ete4.core.operations.Walker.node_id"]], "populate() (in module ete4.core.operations)": [[6, "ete4.core.operations.populate"]], "rehang() (in module ete4.core.operations)": [[6, "ete4.core.operations.rehang"]], "remove() (in module ete4.core.operations)": [[6, "ete4.core.operations.remove"]], "set_outgroup() (in module ete4.core.operations)": [[6, "ete4.core.operations.set_outgroup"]], "sort() (in module ete4.core.operations)": [[6, "ete4.core.operations.sort"]], "swap_props() (in module ete4.core.operations)": [[6, "ete4.core.operations.swap_props"]], "to_ultrametric() (in module ete4.core.operations)": [[6, "ete4.core.operations.to_ultrametric"]], "update_size() (in module ete4.core.operations)": [[6, "ete4.core.operations.update_size"]], "update_sizes_all() (in module ete4.core.operations)": [[6, "ete4.core.operations.update_sizes_all"]], "update_sizes_from() (in module ete4.core.operations)": [[6, "ete4.core.operations.update_sizes_from"]], "walk() (in module ete4.core.operations)": [[6, "ete4.core.operations.walk"]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree"]], "__init__() (phylotree method)": [[7, "ete4.PhyloTree.__init__"]], "annotate_gtdb_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[7, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[7, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[7, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries"]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq"]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries"]], "set_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.set_seq"]], "write() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.write"]], "active (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Active"]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace"]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid"]], "alignmentface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignmentFace"]], "apptree (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.AppTree"]], "arrowface (class in ete4.smartview.renderer.faces)": [[9, 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"ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.modify_tree_fields"]], "name (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (apptree attribute)": [[9, 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"how-do-i-export-tree-images-as-svg"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "Can the visualization of trees with very unbalanced tree branches be improved?": [[1, "can-the-visualization-of-trees-with-very-unbalanced-tree-branches-be-improved"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Contents:": [[2, null]], "Indices and tables": [[2, "indices-and-tables"]], "Reference Guide": [[3, "reference-guide"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "NCBITaxa": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "Tree operations": [[6, "module-ete4.core.operations"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [13, "phylogenetic-trees"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Renderer": [[9, "renderer"]], "Drawer": [[9, 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"adding-taxonomic-information"]], "Automatic control of species info": [[13, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[13, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[13, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[13, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[13, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[13, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[13, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[13, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[13, "implementation"]], "Automatic rooting (outgroup detection)": [[13, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[13, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species 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"ete4.ncbi_taxonomy.ncbiquery": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "get_broken_branches() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_broken_branches"]], "get_common_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_common_names"]], "get_descendant_taxa() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage"]], "get_lineage_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage_translator"]], "get_name_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_name_translator"]], "get_rank() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_rank"]], "get_taxid_translator() (ncbitaxa method)": [[5, 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"ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[7, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[7, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[8, 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"ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb"]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains"]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains"]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName"]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName"]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName"]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, 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"ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__"]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__"]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__"]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__"]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__"]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__"]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__"]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__"]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__"]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__"]], "__init__() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.__init__"]], "__init__() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.__init__"]], "__init__() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.__init__"]], "__init__() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.__init__"]], "__init__() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.__init__"]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__"]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade"]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node"]], "active (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.active"]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face"]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos"]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face"]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend"]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree"]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request"]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer"]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header"]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks"]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions"]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback"]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian"]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name"]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name"]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box"]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box"]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box"]], "compute_bounding_box() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box"]], "compute_bounding_box() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box"]], "compute_bounding_box() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.modify_tree_fields"]], "name (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.searches"]], "selected (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.selected"]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection"]], "style (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get"]], "tree (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.tree"]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "tree (class in ete4)": [[10, "ete4.Tree"]], "__init__() (tree method)": [[10, "ete4.Tree.__init__"]], "add_child() (tree method)": [[10, "ete4.Tree.add_child"]], "add_children() (tree method)": [[10, "ete4.Tree.add_children"]], "add_face() (tree method)": [[10, "ete4.Tree.add_face"]], "add_face_smartview() (tree method)": [[10, "ete4.Tree.add_face_smartview"]], "add_face_treeview() (tree method)": [[10, "ete4.Tree.add_face_treeview"]], "add_feature() (tree method)": [[10, "ete4.Tree.add_feature"]], "add_features() (tree method)": [[10, "ete4.Tree.add_features"]], "add_prop() (tree method)": [[10, "ete4.Tree.add_prop"]], "add_props() (tree method)": [[10, "ete4.Tree.add_props"]], "add_sister() (tree method)": [[10, "ete4.Tree.add_sister"]], "ancestors() (tree method)": [[10, "ete4.Tree.ancestors"]], "check_monophyly() (tree method)": [[10, "ete4.Tree.check_monophyly"]], "children (tree attribute)": [[10, "ete4.Tree.children"]], "collapsed_faces (tree attribute)": [[10, "ete4.Tree.collapsed_faces"]], "common_ancestor() (tree method)": [[10, "ete4.Tree.common_ancestor"]], "compare() (tree method)": [[10, "ete4.Tree.compare"]], "cophenetic_matrix() (tree method)": [[10, "ete4.Tree.cophenetic_matrix"]], "copy() (tree method)": [[10, "ete4.Tree.copy"]], "del_feature() (tree method)": [[10, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[10, "ete4.Tree.del_prop"]], "delete() (tree method)": [[10, "ete4.Tree.delete"]], "descendants() (tree method)": [[10, "ete4.Tree.descendants"]], "describe() (tree method)": [[10, "ete4.Tree.describe"]], "detach() (tree method)": [[10, "ete4.Tree.detach"]], "dist (tree attribute)": [[10, "ete4.Tree.dist"]], "edges() (tree method)": [[10, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[10, "ete4.Tree.expand_polytomies"]], "explore() (tree method)": [[10, "ete4.Tree.explore"]], "faces (tree attribute)": [[10, "ete4.Tree.faces"]], "from_parent_child_table() (tree static method)": [[10, "ete4.Tree.from_parent_child_table"]], "from_skbio() (tree static method)": [[10, "ete4.Tree.from_skbio"]], "get_cached_content() (tree method)": [[10, "ete4.Tree.get_cached_content"]], "get_children() (tree method)": [[10, "ete4.Tree.get_children"]], "get_closest_leaf() (tree method)": [[10, "ete4.Tree.get_closest_leaf"]], "get_distance() (tree method)": [[10, "ete4.Tree.get_distance"]], "get_farthest_leaf() (tree method)": [[10, "ete4.Tree.get_farthest_leaf"]], "get_farthest_node() (tree method)": [[10, "ete4.Tree.get_farthest_node"]], "get_midpoint_outgroup() (tree method)": [[10, "ete4.Tree.get_midpoint_outgroup"]], "get_monophyletic() (tree method)": [[10, "ete4.Tree.get_monophyletic"]], "get_prop() (tree method)": [[10, "ete4.Tree.get_prop"]], "get_sisters() (tree method)": [[10, "ete4.Tree.get_sisters"]], "get_topology_id() (tree method)": [[10, "ete4.Tree.get_topology_id"]], "id (tree attribute)": [[10, "ete4.Tree.id"]], "img_style (tree property)": [[10, "ete4.Tree.img_style"]], "init_from_ete() (tree method)": [[10, "ete4.Tree.init_from_ete"]], "init_from_newick() (tree method)": [[10, "ete4.Tree.init_from_newick"]], "is_collapsed (tree property)": [[10, "ete4.Tree.is_collapsed"]], "is_initialized (tree property)": [[10, "ete4.Tree.is_initialized"]], "is_leaf (tree attribute)": [[10, "ete4.Tree.is_leaf"]], "is_monophyletic() (tree method)": [[10, "ete4.Tree.is_monophyletic"]], "is_root (tree attribute)": [[10, "ete4.Tree.is_root"]], "iter_prepostorder() (tree method)": [[10, "ete4.Tree.iter_prepostorder"]], "ladderize() (tree method)": [[10, "ete4.Tree.ladderize"]], "leaf_names() (tree method)": [[10, "ete4.Tree.leaf_names"]], "leaves() (tree method)": [[10, "ete4.Tree.leaves"]], "level (tree attribute)": [[10, "ete4.Tree.level"]], "lineage() (tree method)": [[10, "ete4.Tree.lineage"]], "name (tree attribute)": [[10, "ete4.Tree.name"]], "phonehome() (tree method)": [[10, "ete4.Tree.phonehome"]], 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a/tutorial/tutorial_phylogeny.html b/tutorial/tutorial_phylogeny.html index 9c2541065..125881051 100644 --- a/tutorial/tutorial_phylogeny.html +++ b/tutorial/tutorial_phylogeny.html @@ -784,7 +784,7 @@
Comparisons between tree topologies provide important information for many evolutionary studies. TreeKO (Marcet and Gabaldon, 2011) @@ -883,7 +883,7 @@
A much simpler approach to separate duplicates within the same gene
family tree is to split the topology by their duplication nodes. For
this, the method PhyloTree.split_by_dups() is provided.
The method PhyloTree.collapse_lineage_specific_expansions()
returns a pruned version of a tree, where nodes representing lineage
specific expansions are converted into a single leaf node.