diff --git a/_sources/tutorial/tutorial_trees.rst.txt b/_sources/tutorial/tutorial_trees.rst.txt index 0394574bb..c4cdb43f9 100644 --- a/_sources/tutorial/tutorial_trees.rst.txt +++ b/_sources/tutorial/tutorial_trees.rst.txt @@ -1386,7 +1386,7 @@ Solving multifurcations When a tree contains a polytomy (a node with more than 2 children), the method :func:`resolve_polytomy` can be used to convert the node -into a randomly bifurcated structure. This is really not a solution +into an arbitrarily bifurcated structure. This is really not a solution for the polytomy but it allows to export the tree as a strictly bifurcated newick structure, which is a requirement for some external software. @@ -1396,7 +1396,7 @@ of the tree intact by disabling the :attr:`recursive` flag. Example:: - t = Tree('(((a,b,c),(d,e,f,g)),(f,i,h));') + t = Tree('(((a,b,c),(d,e,f,g)),(h,i,j));') print(t) # ╭╴a @@ -1406,38 +1406,38 @@ Example:: # │ ╰─┼╴e # ─┤ ├╴f # │ ╰╴g - # │ ╭╴f + # │ ╭╴h # ╰─┼╴i - # ╰╴h + # ╰╴j polynode = t.common_ancestor(['a', 'b']) - polynode.resolve_polytomy(recursive=False) + polynode.resolve_polytomy(descendants=False) print(t) - # ╭─┬╴b - # ╭─┤ ╰╴c - # ╭─┤ ╰╴a + # ╭─┬╴a + # ╭─┤ ╰╴b + # ╭─┤ ╰╴c # │ │ ╭╴d # │ ╰─┼╴e # ─┤ ├╴f # │ ╰╴g - # │ ╭╴f + # │ ╭╴h # ╰─┼╴i - # ╰╴h + # ╰╴j - t.resolve_polytomy(recursive=True) + t.resolve_polytomy(descendants=True) print(t) - # ╭─┬╴b - # ╭─┤ ╰╴c - # │ ╰╴a - # ╭─┤ ╭─┬╴f - # │ │ ╭─┤ ╰╴g - # ─┤ ╰─┤ ╰╴e - # │ ╰╴d - # │ ╭─┬╴i - # ╰─┤ ╰╴h - # ╰╴f + # ╭─┬╴a + # ╭─┤ ╰╴b + # │ ╰╴c + # ╭─┤ ╭─┬╴d + # │ │ ╭─┤ ╰╴e + # ─┤ ╰─┤ ╰╴f + # │ ╰╴g + # │ ╭─┬╴h + # ╰─┤ ╰╴i + # ╰╴j Tree rooting diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html index 1f4ba7b57..955476dfd 100644 --- a/reference/reference_smartview.html +++ b/reference/reference_smartview.html @@ -92,7 +92,7 @@

Smartview (web graphi
-class TreeData(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, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f0749f42a20> = None, searches: dict = None)[source]
+class TreeData(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, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f9fd8d42a20> = 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, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: namedtuple = None, searches: dict = None) → None
diff --git a/reference/reference_tree.html b/reference/reference_tree.html index bbaeeb514..fb6e408d9 100644 --- a/reference/reference_tree.html +++ b/reference/reference_tree.html @@ -901,22 +901,16 @@

Tree (main class)
-resolve_polytomy(self, recursive=True, defaults=None)
-

Resolve all polytomies under the current node, randomly.

+resolve_polytomy(self, descendants=True) +

Convert node to a series of dicotomies if it is a polytomy.

A polytomy is a node that has more than 2 children. This -function resolves them by creating an arbitrary dicotomic -structure among the affected nodes. It randomly modifies the -current tree topology and should only be used for -compatibility reasons (like to later use programs that reject -multifurcated nodes).

+function changes them to a ladderized series of dicotomic +branches. The tree topology modification is arbitrary (no +important results should depend on it!).

Parameters:
-
    -

  • recursive – If True, resolve all polytomies under this -node too. Otherwise, only the current node will be -checked and fixed.

    • -

  • defaults – Dictionary of properties to use for new nodes.

    • -
+

descendants – If True, resolve all polytomies under this +node too. Otherwise, do it only for the current node.

diff --git a/searchindex.js b/searchindex.js index 9a6f34c39..a64008329 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "faqs", "index", "reference/index", "reference/reference_clustering", "reference/reference_operations", "reference/reference_parsers", "reference/reference_phylo", "reference/reference_seqgroup", "reference/reference_smartview", "reference/reference_taxonomy", "reference/reference_tree", "reference/reference_treematcher", "reference/reference_treeview", "tutorial/index", "tutorial/tutorial_phylogeny", "tutorial/tutorial_smartview", "tutorial/tutorial_taxonomy", "tutorial/tutorial_treematcher", "tutorial/tutorial_trees", "tutorial/tutorial_treeview"], "filenames": ["about.rst", "faqs.rst", "index.rst", "reference/index.rst", "reference/reference_clustering.rst", "reference/reference_operations.rst", "reference/reference_parsers.rst", "reference/reference_phylo.rst", "reference/reference_seqgroup.rst", 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19, "The": 19, "mean": 19, "unroot": 19, "travers": 19, "leav": 19, "while": 19, "iter": 19, "list": 19, "given": 19, "criteria": 19, "first": 19, "common": 19, "ancestor": 19, "shortcut": 19, "check": 19, "monophyli": 19, "cach": 19, "faster": 19, "lookup": 19, "compar": 19, "distanc": 19, "robinson": 19, "fould": 19, "modifi": 19, "scratch": 19, "delet": 19, "elimin": 19, "remov": 19, "detach": 19, "prune": 19, "concaten": 19, "solv": 19, "multifurc": 19, "midpoint": 19, "chang": 20, "scale": 20, "zoom": 20, "x": 20, "separ": 20, "y": 20, "rotat": 20, "180": 20, "degre": 20, "titl": 20, "img": 20, "bubbl": 20, "map": 20, "your": 20}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"About": [[0, "about"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "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"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Parsers": [[6, "parsers"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "PhyloTree": [[7, "phylotree"]], "EvolEvent": [[7, "evolevent"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Renderer": [[9, "renderer"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Layouts": [[9, "layouts"]], "context": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "NCBITaxa": [[10, "ncbitaxa"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "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"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Standalone scripts": [[16, "standalone-scripts"]], "Interactive sessions": [[16, "interactive-sessions"]], "Verbose mode": [[16, "verbose-mode"]], "Show leaf node names, branch length and branch support": [[16, "show-leaf-node-names-branch-length-and-branch-support"], [20, "show-leaf-node-names-branch-length-and-branch-support"]], "Showing node\u2019s properties in pop up": [[16, "showing-node-s-properties-in-pop-up"]], "Control Panel": [[16, "control-panel"]], "1) Layout Tab": [[16, "layout-tab"]], "Overrall": [[16, "overrall"]], "Download": [[16, "download"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "Simple search": [[16, "simple-search"]], "Regular expression search": [[16, "regular-expression-search"]], "Expression search": [[16, "expression-search"]], "Topological search": [[16, "topological-search"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "3) Advanced Tab": [[16, "advanced-tab"]], "Node Panel": [[16, "node-panel"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Add legend": [[16, "add-legend"]], "Node style": [[16, "node-style"], [20, "node-style"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Color Strip": [[16, "color-strip"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Bar Plot": [[16, "bar-plot"]], "Heatmap": [[16, "heatmap"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Domain annotation": [[16, "domain-annotation"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Getting taxid information": [[17, "getting-taxid-information"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "Outside variables": [[18, "outside-variables"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Trees": [[19, "trees"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Writing newick trees": [[19, "writing-newick-trees"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Advanced traversing": [[19, "advanced-traversing"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Search all nodes matching a given criteria": [[19, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria": [[19, "search-nodes-matching-a-given-criteria"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Shortcuts": [[19, "shortcuts"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[19, "node-annotation"]], "Comparing trees": [[19, "comparing-trees"]], "Distances between trees": [[19, "distances-between-trees"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[19, "pruning-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Tree rooting": [[19, "tree-rooting"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Tree style": [[20, "tree-style"]], "Change branch length scale (zoom in x)": [[20, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[20, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[20, "rotate-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Add legend and title": [[20, "add-legend-and-title"]], "Layout functions": [[20, "layout-functions"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Node backgrounds": [[20, "node-backgrounds"]], "Img faces": [[20, "img-faces"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Trees within trees": [[20, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]]}, "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.core.operations"], [6, "module-ete4.parser.newick"], [6, "module-ete4.parser.nexus"], [8, "module-ete4.core.seqgroup"], [9, "module-ete4.smartview.gui.server"], [9, "module-ete4.smartview.renderer.draw_helpers"], [9, "module-ete4.smartview.renderer.drawer"], [9, "module-ete4.smartview.renderer.face_positions"], [9, "module-ete4.smartview.renderer.faces"], [9, "module-ete4.smartview.renderer.layouts.context_layouts"], [9, "module-ete4.smartview.renderer.layouts.default_layouts"], [9, "module-ete4.smartview.renderer.layouts.domain_layouts"], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [9, "module-ete4.smartview.renderer.layouts.seq_layouts"], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [9, "module-ete4.smartview.renderer.layouts.staple_layouts"], [9, "module-ete4.smartview.renderer.nodestyle"], [9, "module-ete4.smartview.renderer.treelayout"], [9, "module-ete4.smartview.renderer.treestyle"], [12, "module-ete4.treematcher.treematcher"], [13, "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"]], "walker (class in ete4.core.operations)": [[5, "ete4.core.operations.Walker"]], "add_branch_values() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_branch_values"]], "add_leaf_names() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_leaf_names"]], "add_next_branch() (walker method)": [[5, "ete4.core.operations.Walker.add_next_branch"]], "assert_root_consistency() (in module ete4.core.operations)": [[5, "ete4.core.operations.assert_root_consistency"]], "common_ancestor() (in module ete4.core.operations)": [[5, "ete4.core.operations.common_ancestor"]], "create_dichotomic_sister() (in module ete4.core.operations)": [[5, "ete4.core.operations.create_dichotomic_sister"]], "ete4.core.operations": [[5, "module-ete4.core.operations"]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit"]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back"]], 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"ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName.__init__"]], "__init__() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.__init__"]], "__init__() (layoutsmartdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains.__init__"]], "__init__() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.__init__"]], "__init__() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__"]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__"]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__"]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__"]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__"]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__"]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__"]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__"]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__"]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__"]], "__init__() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.__init__"]], "__init__() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.__init__"]], "__init__() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.__init__"]], "__init__() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.__init__"]], "__init__() (treedata method)": [[9, "ete4.smartview.gui.server.TreeData.__init__"]], "__init__() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.__init__"]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__"]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade"]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node"]], "active (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.active"]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face"]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos"]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face"]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend"]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree"]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request"]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer"]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header"]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks"]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions"]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback"]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian"]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name"]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name"]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box"]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box"]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box"]], "compute_bounding_box() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box"]], "compute_bounding_box() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box"]], "compute_bounding_box() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.modify_tree_fields"]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches"]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected"]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection"]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get"]], "tree (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.tree"]], "ultrametric (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.ultrametric"]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa"]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa"]], "__init__() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.__init__"]], "__init__() (ncbitaxa method)": [[10, "ete4.NCBITaxa.__init__"]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree"]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree"]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches"]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches"]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names"]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names"]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa"]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage"]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage"]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator"]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator"]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage"]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator"]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator"]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank"]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank"]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator"]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator"]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology"]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology"]], "translate_to_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.translate_to_names"]], "translate_to_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.update_taxonomy_database"]], "update_taxonomy_database() (ncbitaxa method)": [[10, "ete4.NCBITaxa.update_taxonomy_database"]], "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"]], 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"sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"About": [[0, "about"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "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"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Parsers": [[6, "parsers"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "PhyloTree": [[7, "phylotree"]], "EvolEvent": [[7, "evolevent"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Renderer": [[9, "renderer"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Layouts": [[9, "layouts"]], "context": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "NCBITaxa": [[10, "ncbitaxa"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "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"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Standalone scripts": [[16, "standalone-scripts"]], "Interactive sessions": [[16, "interactive-sessions"]], "Verbose mode": [[16, "verbose-mode"]], "Show leaf node names, branch length and branch support": [[16, "show-leaf-node-names-branch-length-and-branch-support"], [20, "show-leaf-node-names-branch-length-and-branch-support"]], "Showing node\u2019s properties in pop up": [[16, "showing-node-s-properties-in-pop-up"]], "Control Panel": [[16, "control-panel"]], "1) Layout Tab": [[16, "layout-tab"]], "Overrall": [[16, "overrall"]], "Download": [[16, "download"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "Simple search": [[16, "simple-search"]], "Regular expression search": [[16, "regular-expression-search"]], "Expression search": [[16, "expression-search"]], "Topological search": [[16, "topological-search"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "3) Advanced Tab": [[16, "advanced-tab"]], "Node Panel": [[16, "node-panel"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Add legend": [[16, "add-legend"]], "Node style": [[16, "node-style"], [20, "node-style"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Color Strip": [[16, "color-strip"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Bar Plot": [[16, "bar-plot"]], "Heatmap": [[16, "heatmap"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Domain annotation": [[16, "domain-annotation"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Getting taxid information": [[17, "getting-taxid-information"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "Outside variables": [[18, "outside-variables"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Trees": [[19, "trees"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Writing newick trees": [[19, "writing-newick-trees"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Advanced traversing": [[19, "advanced-traversing"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Search all nodes matching a given criteria": [[19, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria": [[19, "search-nodes-matching-a-given-criteria"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Shortcuts": [[19, "shortcuts"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[19, "node-annotation"]], "Comparing trees": [[19, "comparing-trees"]], "Distances between trees": [[19, "distances-between-trees"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[19, "pruning-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Tree rooting": [[19, "tree-rooting"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Tree style": [[20, "tree-style"]], "Change branch length scale (zoom in x)": [[20, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[20, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[20, "rotate-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Add legend and title": [[20, "add-legend-and-title"]], "Layout functions": [[20, "layout-functions"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Node backgrounds": [[20, "node-backgrounds"]], "Img faces": [[20, "img-faces"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Trees within trees": [[20, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]]}, "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, 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"ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.__init__"]], "__init__() (layoutscientificname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName.__init__"]], "__init__() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.__init__"]], "__init__() (layoutsmartdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains.__init__"]], "__init__() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.__init__"]], "__init__() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__"]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__"]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__"]], "__init__() (outlineface method)": [[9, 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"ete4.smartview.renderer.treestyle.TreeStyle.add_legend"]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree"]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request"]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer"]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header"]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks"]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions"]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback"]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian"]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name"]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name"]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[9, 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method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[9, 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ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.modify_tree_fields"]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches"]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected"]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection"]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get"]], "tree (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.tree"]], "ultrametric (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.ultrametric"]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa"]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa"]], "__init__() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.__init__"]], "__init__() (ncbitaxa method)": [[10, "ete4.NCBITaxa.__init__"]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree"]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree"]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches"]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches"]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names"]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names"]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa"]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage"]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage"]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator"]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator"]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage"]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator"]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator"]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank"]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank"]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator"]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator"]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology"]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology"]], "translate_to_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.translate_to_names"]], "translate_to_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.update_taxonomy_database"]], "update_taxonomy_database() (ncbitaxa method)": [[10, "ete4.NCBITaxa.update_taxonomy_database"]], "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, 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"ete4.treematcher.treematcher.match"]], "safer_eval() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.safer_eval"]], "search() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.search"]], "search() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.search"]], "treeview": [[13, "module-treeview"]]}}) \ No newline at end of file diff --git a/tutorial/tutorial_trees.html b/tutorial/tutorial_trees.html index 394e0dd67..ddda99691 100644 --- a/tutorial/tutorial_trees.html +++ b/tutorial/tutorial_trees.html @@ -1476,14 +1476,14 @@

Concatenating trees<

Solving multifurcations

When a tree contains a polytomy (a node with more than 2 children), the method resolve_polytomy() can be used to convert the node -into a randomly bifurcated structure. This is really not a solution +into an arbitrarily bifurcated structure. This is really not a solution for the polytomy but it allows to export the tree as a strictly bifurcated newick structure, which is a requirement for some external software.

The method can be used on a very specific node while keeping the rest of the tree intact by disabling the recursive flag.

Example:

-
t = Tree('(((a,b,c),(d,e,f,g)),(f,i,h));')
+
t = Tree('(((a,b,c),(d,e,f,g)),(h,i,j));')
 
 print(t)
 #      ╭╴a
@@ -1493,38 +1493,38 @@ 
Concatenating trees<
 #  │ ╰─┼╴e
 # ─┤   ├╴f
 #  │   ╰╴g
-#  │ ╭╴f
+#  │ ╭╴h
 #  ╰─┼╴i
-#    ╰╴h
+#    ╰╴j
 
 polynode = t.common_ancestor(['a', 'b'])
-polynode.resolve_polytomy(recursive=False)
+polynode.resolve_polytomy(descendants=False)
 
 print(t)
-#      ╭─┬╴b
-#    ╭─┤ ╰╴c
-#  ╭─┤ ╰╴a
+#      ╭─┬╴a
+#    ╭─┤ ╰╴b
+#  ╭─┤ ╰╴c
 #  │ │ ╭╴d
 #  │ ╰─┼╴e
 # ─┤   ├╴f
 #  │   ╰╴g
-#  │ ╭╴f
+#  │ ╭╴h
 #  ╰─┼╴i
-#    ╰╴h
+#    ╰╴j
 
-t.resolve_polytomy(recursive=True)
+t.resolve_polytomy(descendants=True)
 
 print(t)
-#      ╭─┬╴b
-#    ╭─┤ ╰╴c
-#    │ ╰╴a
-#  ╭─┤   ╭─┬╴f
-#  │ │ ╭─┤ ╰╴g
-# ─┤ ╰─┤ ╰╴e
-#  │   ╰╴d
-#  │ ╭─┬╴i
-#  ╰─┤ ╰╴h
-#    ╰╴f
+#      ╭─┬╴a
+#    ╭─┤ ╰╴b
+#    │ ╰╴c
+#  ╭─┤   ╭─┬╴d
+#  │ │ ╭─┤ ╰╴e
+# ─┤ ╰─┤ ╰╴f
+#  │   ╰╴g
+#  │ ╭─┬╴h
+#  ╰─┤ ╰╴i
+#    ╰╴j