From 01b40c915b434598db01017fcb31104e89f1eb72 Mon Sep 17 00:00:00 2001 From: jordibc Date: Wed, 25 Oct 2023 08:47:39 +0000 Subject: [PATCH] deploy: 71477476f2ab9aed409479510911ace68aadb5c2 --- reference/reference_smartview.html | 2 +- searchindex.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html index 5a8df6409..ac42321e4 100644 --- a/reference/reference_smartview.html +++ b/reference/reference_smartview.html @@ -86,7 +86,7 @@

Smartview (web graphi
-class AppTree(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7fd39b31b2e0> = None, searches: dict = None)[source]
+class AppTree(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f9514d1b2e0> = None, searches: dict = None)[source]
__init__(tree: Tree = None, name: str = None, style: TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, initialized: bool = False, selected: dict = None, active: namedtuple = None, searches: dict = None) → None
diff --git a/searchindex.js b/searchindex.js index 62945d3e2..d5f7de387 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "faqs", "index", "reference/index", "reference/reference_clustering", "reference/reference_ncbi", "reference/reference_operations", "reference/reference_parsers", "reference/reference_phylo", "reference/reference_seqgroup", "reference/reference_smartview", "reference/reference_tree", "reference/reference_treeview", "tutorial/index", "tutorial/tutorial_drawing", "tutorial/tutorial_phylogeny", "tutorial/tutorial_trees"], "filenames": ["about.rst", "faqs.rst", "index.rst", "reference/index.rst", "reference/reference_clustering.rst", "reference/reference_ncbi.rst", "reference/reference_operations.rst", "reference/reference_parsers.rst", "reference/reference_phylo.rst", "reference/reference_seqgroup.rst", "reference/reference_smartview.rst", "reference/reference_tree.rst", "reference/reference_treeview.rst", "tutorial/index.rst", "tutorial/tutorial_drawing.rst", "tutorial/tutorial_phylogeny.rst", "tutorial/tutorial_trees.rst"], "titles": ["About", "Frequently Asked Questions (FAQs)", "Welcome to ETE\u2019s documentation!", "Reference Guide", "Clustering", "NCBITaxa", "Tree operations", "Parsers", "Phylogenetic trees", "Multiple Sequence Alignments (SeqGroup)", "Smartview (web graphics)", "Tree (main class)", "Treeview (qt graphics)", "ETE Tutorial", "Programmable tree drawing", "Phylogenetic trees", "Working with the Tree structure"], "terms": {"The": [0, 1, 5, 6, 8, 10, 11, 14, 15], "toolkit": [0, 14, 16], "wa": [0, 7, 14, 16], "origin": [0, 6, 8, 11, 14, 15, 16], "develop": 0, "bioinformat": [0, 8, 16], "depart": 0, "cipf": 0, "valencia": 0, "spain": 0, "greatli": 0, "improv": [0, 15], "compar": [0, 11, 13, 15], "genom": [0, 8, 10, 15], "group": [0, 5, 8, 11, 15, 16], "crg": 0, "barcelona": 0, "structur": [0, 2, 4, 8, 10, 11, 13, 14, 15], "comput": [0, 4, 10, 11, 16], "biologi": [0, 15], 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[16, "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"]], "Parsers": [[7, "parsers"]], "Newick": [[7, "module-ete4.parser.newick"]], "Nexus": [[7, "module-ete4.parser.nexus"]], "Phylogenetic trees": [[8, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "Multiple Sequence Alignments (SeqGroup)": [[9, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[10, "smartview-web-graphics"]], "Server": [[10, "module-ete4.smartview.gui.server"]], "Renderer": [[10, "renderer"]], "Drawer": [[10, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[10, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[10, "module-ete4.smartview.renderer.faces"], [12, "faces"]], "Face positions": [[10, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[10, "module-ete4.smartview.renderer.nodestyle"], [12, "nodestyle"]], "TreeLayout": [[10, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[10, "module-ete4.smartview.renderer.treestyle"], [12, "treestyle"]], "Layouts": [[10, "layouts"]], "context": [[10, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[10, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[10, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[10, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[10, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[10, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Tree (main class)": [[11, "tree-main-class"]], "Treeview (qt graphics)": [[12, "treeview-qt-graphics"]], "ETE Tutorial": [[13, "ete-tutorial"]], "Programmable tree drawing": [[14, "programmable-tree-drawing"]], "Overview": [[14, "overview"], [15, "overview"]], "Interactive visualization of trees": [[14, "interactive-visualization-of-trees"]], "Rendering trees as images": [[14, "rendering-trees-as-images"]], "Customizing the aspect of trees": [[14, "customizing-the-aspect-of-trees"]], "Tree style": [[14, "tree-style"]], "Show leaf node names, branch length and branch support": [[14, "show-leaf-node-names-branch-length-and-branch-support"]], "Change branch length scale (zoom in x)": [[14, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[14, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[14, "rotate-a-tree"]], "Circular tree in 180 degrees": [[14, "circular-tree-in-180-degrees"]], "Add legend and title": [[14, "add-legend-and-title"]], "Node style": [[14, "node-style"]], "Node faces": [[14, "node-faces"]], "Faces position": [[14, "faces-position"]], "Face properties": [[14, "face-properties"]], "Layout functions": [[14, "layout-functions"]], "Combining styles, faces and layouts": [[14, "combining-styles-faces-and-layouts"]], "Fixed node styles": [[14, "fixed-node-styles"]], "Node backgrounds": [[14, "node-backgrounds"]], "Img faces": [[14, "img-faces"]], "Bubble tree maps": [[14, "bubble-tree-maps"]], "Trees within trees": [[14, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[14, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[14, "creating-your-custom-interactive-faces"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[15, "implementation"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Working with the Tree structure": [[16, "working-with-the-tree-structure"]], "Trees": [[16, "trees"]], "Reading and writing newick trees": [[16, "reading-and-writing-newick-trees"]], "Creating a tree": [[16, "creating-a-tree"]], "Reading newick trees": [[16, "reading-newick-trees"]], "Writing newick trees": [[16, "writing-newick-trees"]], "Understanding ETE trees": [[16, "understanding-ete-trees"]], "Basic tree attributes": [[16, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[16, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[16, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[16, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[16, "traversing-browsing-trees"]], "Advanced traversing": [[16, "advanced-traversing"]], "Collapsing nodes while traversing": [[16, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[16, "iterators-or-lists"]], "Finding nodes by their properties": [[16, "finding-nodes-by-their-properties"]], "Search_all nodes matching a given criteria": [[16, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria (iteration)": [[16, "search-nodes-matching-a-given-criteria-iteration"]], "Find the first common ancestor": [[16, "find-the-first-common-ancestor"]], "Custom searching functions": [[16, "custom-searching-functions"]], "Shortcuts": [[16, "shortcuts"]], "Checking the monophyly of properties within a tree": [[16, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[16, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[16, "node-annotation"]], "Comparing trees": [[16, "comparing-trees"]], "Distances between trees": [[16, "distances-between-trees"]], "Robinson-Foulds distance": [[16, "robinson-foulds-distance"]], "Modifying tree topology": [[16, "modifying-tree-topology"]], "Creating trees from scratch": [[16, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[16, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[16, "pruning-trees"]], "Concatenating trees": [[16, "concatenating-trees"]], "Copying (duplicating) trees": [[16, "copying-duplicating-trees"]], "Solving multifurcations": [[16, "solving-multifurcations"]], "Tree rooting": [[16, "tree-rooting"]], "Working with branch distances": [[16, "working-with-branch-distances"]], "Getting distances between nodes": [[16, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[16, "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"], [7, "module-ete4.parser.newick"], [7, "module-ete4.parser.nexus"], [9, "module-ete4.core.seqgroup"], [10, "module-ete4.smartview.gui.server"], [10, "module-ete4.smartview.renderer.draw_helpers"], [10, "module-ete4.smartview.renderer.drawer"], [10, "module-ete4.smartview.renderer.face_positions"], [10, "module-ete4.smartview.renderer.faces"], [10, "module-ete4.smartview.renderer.layouts.context_layouts"], [10, "module-ete4.smartview.renderer.layouts.default_layouts"], [10, "module-ete4.smartview.renderer.layouts.domain_layouts"], [10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [10, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [10, "module-ete4.smartview.renderer.layouts.seq_layouts"], [10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [10, "module-ete4.smartview.renderer.layouts.staple_layouts"], [10, "module-ete4.smartview.renderer.nodestyle"], [10, "module-ete4.smartview.renderer.treelayout"], [10, "module-ete4.smartview.renderer.treestyle"], [12, "module-treeview"]], "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"]], "newickerror": [[7, "ete4.parser.newick.NewickError"]], "nexuserror": [[7, "ete4.parser.nexus.NexusError"]], "apply_translations() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.apply_translations"]], "content_repr() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.content_repr"]], "dump() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.dump"]], "dumps() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.dumps"]], "error() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.error"]], "ete4.parser.newick": [[7, "module-ete4.parser.newick"]], "ete4.parser.nexus": [[7, "module-ete4.parser.nexus"]], "get_commands() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_commands"]], "get_extended_props() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.get_extended_props"]], "get_props() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.get_props"]], "get_section() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_section"]], "get_sections() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_sections"]], "get_trees() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_trees"]], "load() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.load"]], "load() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.load"]], "loads() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.loads"]], "loads() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.loads"]], "make_parser() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.make_parser"]], "prop_repr() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.prop_repr"]], "quote() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.quote"]], "read_content() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.read_content"]], "read_nodes() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.read_nodes"]], "repr_short() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.repr_short"]], "skip_quoted_name() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.skip_quoted_name"]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.skip_spaces_and_comments"]], "unquote() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.unquote"]], "evolevent (class in ete4.phylo)": [[8, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[8, "ete4.PhyloTree"]], "__init__() (phylotree method)": [[8, "ete4.PhyloTree.__init__"]], "annotate_gtdb_taxa() (phylotree method)": [[8, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[8, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[8, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[8, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[8, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[8, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[8, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[8, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[8, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[8, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[8, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[8, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[8, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[8, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[8, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[8, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[8, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[8, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[8, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[9, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[9, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[9, 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"ete4.smartview.renderer.faces.ArrowFace"]], "attrface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AttrFace"]], "box (class in ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.Box"]], "collapse_size (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE"]], "circleface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.CircleFace"]], "drawer (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.Drawer"]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces"]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces"]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc"]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[10, 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"ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[10, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[10, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], "compute_bounding_box() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box"]], "compute_bounding_box() (rectface method)": [[10, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box"]], "compute_bounding_box() (scaleface method)": [[10, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box"]], "compute_bounding_box() (seqface method)": [[10, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box"]], "compute_bounding_box() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box"]], "compute_bounding_box() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[10, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[10, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[10, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[10, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[10, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[10, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[10, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[10, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[10, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[10, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[10, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[10, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[10, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[10, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[10, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[10, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[10, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[10, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[10, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[10, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[10, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[10, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[10, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[10, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[10, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[10, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[10, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[10, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[10, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[10, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [10, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[10, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[10, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[10, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_newick"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[10, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.include_props"]], "init() (nodestyle method)": [[10, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.json_error"]], "layouts (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.modify_tree_fields"]], "name (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[10, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.nodestyles"]], "on_first_visit() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[10, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[10, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[10, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[10, 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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, 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"module-ete4.smartview.renderer.layouts.staple_layouts"]], "Tree (main class)": [[11, "tree-main-class"]], "Treeview (qt graphics)": [[12, "treeview-qt-graphics"]], "ETE Tutorial": [[13, "ete-tutorial"]], "Programmable tree drawing": [[14, "programmable-tree-drawing"]], "Overview": [[14, "overview"], [15, "overview"]], "Interactive visualization of trees": [[14, "interactive-visualization-of-trees"]], "Rendering trees as images": [[14, "rendering-trees-as-images"]], "Customizing the aspect of trees": [[14, "customizing-the-aspect-of-trees"]], "Tree style": [[14, "tree-style"]], "Show leaf node names, branch length and branch support": [[14, "show-leaf-node-names-branch-length-and-branch-support"]], "Change branch length scale (zoom in x)": [[14, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[14, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[14, "rotate-a-tree"]], "Circular tree in 180 degrees": [[14, "circular-tree-in-180-degrees"]], "Add legend and title": [[14, "add-legend-and-title"]], "Node style": [[14, "node-style"]], "Node faces": [[14, "node-faces"]], "Faces position": [[14, "faces-position"]], "Face properties": [[14, "face-properties"]], "Layout functions": [[14, "layout-functions"]], "Combining styles, faces and layouts": [[14, "combining-styles-faces-and-layouts"]], "Fixed node styles": [[14, "fixed-node-styles"]], "Node backgrounds": [[14, "node-backgrounds"]], "Img faces": [[14, "img-faces"]], "Bubble tree maps": [[14, "bubble-tree-maps"]], "Trees within trees": [[14, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[14, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[14, "creating-your-custom-interactive-faces"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[15, "implementation"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Working with the Tree structure": [[16, "working-with-the-tree-structure"]], "Trees": [[16, "trees"]], "Reading and writing newick trees": [[16, "reading-and-writing-newick-trees"]], "Creating a tree": [[16, "creating-a-tree"]], "Reading newick trees": [[16, "reading-newick-trees"]], "Writing newick trees": [[16, "writing-newick-trees"]], "Understanding ETE trees": [[16, "understanding-ete-trees"]], "Basic tree attributes": [[16, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[16, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[16, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[16, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[16, "traversing-browsing-trees"]], "Advanced traversing": [[16, "advanced-traversing"]], "Collapsing nodes while traversing": [[16, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[16, "iterators-or-lists"]], "Finding nodes by their properties": [[16, "finding-nodes-by-their-properties"]], "Search_all nodes matching a given criteria": [[16, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria (iteration)": [[16, "search-nodes-matching-a-given-criteria-iteration"]], "Find the first common ancestor": [[16, "find-the-first-common-ancestor"]], "Custom searching functions": [[16, "custom-searching-functions"]], "Shortcuts": [[16, "shortcuts"]], "Checking the monophyly of properties within a tree": [[16, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[16, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[16, "node-annotation"]], "Comparing trees": [[16, "comparing-trees"]], "Distances between trees": [[16, "distances-between-trees"]], "Robinson-Foulds distance": [[16, "robinson-foulds-distance"]], "Modifying tree topology": [[16, "modifying-tree-topology"]], "Creating trees from scratch": [[16, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[16, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[16, "pruning-trees"]], "Concatenating trees": [[16, "concatenating-trees"]], "Copying (duplicating) trees": [[16, "copying-duplicating-trees"]], "Solving multifurcations": [[16, "solving-multifurcations"]], "Tree rooting": [[16, "tree-rooting"]], "Working with branch distances": [[16, "working-with-branch-distances"]], "Getting distances between nodes": [[16, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[16, "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"], [7, "module-ete4.parser.newick"], [7, "module-ete4.parser.nexus"], [9, "module-ete4.core.seqgroup"], [10, "module-ete4.smartview.gui.server"], [10, "module-ete4.smartview.renderer.draw_helpers"], [10, "module-ete4.smartview.renderer.drawer"], [10, "module-ete4.smartview.renderer.face_positions"], [10, "module-ete4.smartview.renderer.faces"], [10, "module-ete4.smartview.renderer.layouts.context_layouts"], [10, "module-ete4.smartview.renderer.layouts.default_layouts"], [10, "module-ete4.smartview.renderer.layouts.domain_layouts"], [10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [10, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [10, "module-ete4.smartview.renderer.layouts.seq_layouts"], [10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [10, "module-ete4.smartview.renderer.layouts.staple_layouts"], [10, "module-ete4.smartview.renderer.nodestyle"], [10, "module-ete4.smartview.renderer.treelayout"], [10, "module-ete4.smartview.renderer.treestyle"], [12, "module-treeview"]], "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"]], "newickerror": [[7, "ete4.parser.newick.NewickError"]], "nexuserror": [[7, "ete4.parser.nexus.NexusError"]], "apply_translations() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.apply_translations"]], "content_repr() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.content_repr"]], "dump() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.dump"]], "dumps() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.dumps"]], "error() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.error"]], "ete4.parser.newick": [[7, "module-ete4.parser.newick"]], "ete4.parser.nexus": [[7, "module-ete4.parser.nexus"]], "get_commands() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_commands"]], "get_extended_props() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.get_extended_props"]], "get_props() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.get_props"]], "get_section() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_section"]], "get_sections() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_sections"]], "get_trees() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_trees"]], "load() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.load"]], "load() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.load"]], "loads() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.loads"]], "loads() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.loads"]], "make_parser() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.make_parser"]], "prop_repr() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.prop_repr"]], "quote() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.quote"]], "read_content() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.read_content"]], "read_nodes() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.read_nodes"]], "repr_short() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.repr_short"]], "skip_quoted_name() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.skip_quoted_name"]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.skip_spaces_and_comments"]], "unquote() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.unquote"]], "evolevent (class in ete4.phylo)": [[8, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[8, "ete4.PhyloTree"]], "__init__() (phylotree method)": [[8, "ete4.PhyloTree.__init__"]], "annotate_gtdb_taxa() (phylotree method)": [[8, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[8, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[8, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[8, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[8, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[8, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[8, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[8, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[8, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[8, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[8, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[8, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[8, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[8, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[8, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[8, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[8, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[8, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[8, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[9, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[9, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.get_entries"]], "get_seq() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.get_seq"]], "iter_entries() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.iter_entries"]], "set_seq() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.set_seq"]], "write() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.write"]], "active (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.Active"]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace"]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.AlignedGrid"]], "alignmentface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AlignmentFace"]], "apptree (class in ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.AppTree"]], "arrowface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.ArrowFace"]], "attrface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AttrFace"]], "box (class in ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.Box"]], "collapse_size (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE"]], "circleface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.CircleFace"]], "drawer (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.Drawer"]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces"]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces"]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc"]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces"]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerRect"]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces"]], "face (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.Face"]], "globalstuff (class in ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.GlobalStuff"]], "grid (class in ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.Grid"]], "htmlface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.HTMLFace"]], "imgface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.ImgFace"]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment"]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName"]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[10, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot"]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName"]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg"]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength"]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport"]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard"]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy"]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName"]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[10, 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"ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme"]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule"]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber"]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway"]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor"]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[10, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor"]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[10, 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"layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName"]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName"]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName"]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[10, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains"]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC"]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans"]], "legendface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.LegendFace"]], "min_size (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE"]], "npanels (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.NPANELS"]], "npanels (draweraligncircfaces attribute)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS"]], "npanels (draweralignrectfaces attribute)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS"]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[10, "ete4.smartview.renderer.nodestyle.NodeStyle"]], "outlineface (class in ete4.smartview.renderer.faces)": [[10, 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"ete4.smartview.gui.server.change_selection_name"]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[10, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[10, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[10, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], 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"ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[10, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[10, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[10, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[10, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[10, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[10, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[10, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[10, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[10, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[10, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[10, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[10, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[10, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[10, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[10, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[10, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[10, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[10, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[10, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[10, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[10, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[10, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[10, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[10, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[10, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[10, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[10, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[10, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [10, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[10, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[10, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[10, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_newick"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[10, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.include_props"]], "init() (nodestyle method)": [[10, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.json_error"]], "layouts (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.modify_tree_fields"]], "name (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[10, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.nodestyles"]], "on_first_visit() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[10, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[10, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[10, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.search_to_selection"]], "searches (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.searches"]], "selected (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.selected"]], "selected_face (treestyle property)": [[10, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[10, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[10, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[10, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [10, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [10, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[10, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[10, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [10, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[10, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.store_selection"]], "style (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.touch_and_get"]], "tree (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.tree"]], "unselect_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "tree (class in ete4)": [[11, "ete4.Tree"]], "__init__() (tree method)": [[11, "ete4.Tree.__init__"]], "add_child() (tree method)": [[11, "ete4.Tree.add_child"]], "add_children() (tree method)": [[11, "ete4.Tree.add_children"]], "add_face() (tree method)": [[11, "ete4.Tree.add_face"]], "add_face_smartview() (tree method)": [[11, "ete4.Tree.add_face_smartview"]], "add_face_treeview() (tree method)": [[11, "ete4.Tree.add_face_treeview"]], "add_feature() (tree method)": [[11, "ete4.Tree.add_feature"]], "add_features() (tree method)": [[11, "ete4.Tree.add_features"]], "add_prop() (tree method)": [[11, "ete4.Tree.add_prop"]], "add_props() (tree method)": [[11, "ete4.Tree.add_props"]], "add_sister() (tree method)": [[11, "ete4.Tree.add_sister"]], "ancestors() (tree method)": [[11, "ete4.Tree.ancestors"]], "check_monophyly() (tree method)": [[11, "ete4.Tree.check_monophyly"]], "children (tree attribute)": [[11, "ete4.Tree.children"]], "collapsed_faces (tree attribute)": [[11, "ete4.Tree.collapsed_faces"]], "common_ancestor() (tree method)": [[11, "ete4.Tree.common_ancestor"]], "compare() (tree method)": [[11, "ete4.Tree.compare"]], "cophenetic_matrix() (tree method)": [[11, "ete4.Tree.cophenetic_matrix"]], "copy() (tree method)": [[11, "ete4.Tree.copy"]], "del_feature() (tree method)": [[11, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop"]], "delete() (tree method)": [[11, "ete4.Tree.delete"]], "descendants() (tree method)": [[11, "ete4.Tree.descendants"]], "describe() (tree method)": [[11, "ete4.Tree.describe"]], "detach() (tree method)": [[11, "ete4.Tree.detach"]], "dist (tree attribute)": [[11, "ete4.Tree.dist"]], "edges() (tree method)": [[11, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies"]], "explore() (tree method)": [[11, "ete4.Tree.explore"]], "faces (tree attribute)": [[11, "ete4.Tree.faces"]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table"]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio"]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content"]], "get_children() (tree method)": [[11, "ete4.Tree.get_children"]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf"]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance"]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf"]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node"]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup"]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic"]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop"]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters"]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id"]], "id (tree attribute)": [[11, "ete4.Tree.id"]], "img_style (tree property)": [[11, "ete4.Tree.img_style"]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete"]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick"]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed"]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized"]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf"]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic"]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root"]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder"]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize"]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names"]], "leaves() (tree method)": [[11, "ete4.Tree.leaves"]], "level (tree attribute)": [[11, "ete4.Tree.level"]], "lineage() (tree method)": [[11, "ete4.Tree.lineage"]], "name (tree attribute)": [[11, "ete4.Tree.name"]], "phonehome() (tree method)": [[11, "ete4.Tree.phonehome"]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child"]], "populate() (tree method)": [[11, "ete4.Tree.populate"]], "props (tree attribute)": [[11, "ete4.Tree.props"]], "prune() (tree method)": [[11, "ete4.Tree.prune"]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child"]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children"]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister"]], "render() (tree method)": [[11, "ete4.Tree.render"]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy"]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children"]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds"]], "root (tree attribute)": [[11, "ete4.Tree.root"]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors"]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants"]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name"]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes"]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup"]], "set_style() (tree method)": [[11, "ete4.Tree.set_style"]], "show() (tree method)": [[11, "ete4.Tree.show"]], "size (tree attribute)": [[11, "ete4.Tree.size"]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style"]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants"]], "standardize() (tree method)": [[11, "ete4.Tree.standardize"]], "support (tree attribute)": [[11, "ete4.Tree.support"]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children"]], "to_str() (tree method)": [[11, "ete4.Tree.to_str"]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric"]], "traverse() (tree method)": [[11, "ete4.Tree.traverse"]], "unroot() (tree method)": [[11, "ete4.Tree.unroot"]], "up (tree attribute)": [[11, "ete4.Tree.up"]], "write() (tree method)": [[11, "ete4.Tree.write"]], "treeview": [[12, "module-treeview"]]}}) \ No newline at end of file