diff --git a/_modules/ete4/smartview/gui/server.html b/_modules/ete4/smartview/gui/server.html index eae67fb6..38fc843f 100644 --- a/_modules/ete4/smartview/gui/server.html +++ b/_modules/ete4/smartview/gui/server.html @@ -801,11 +801,20 @@

Source code for ete4.smartview.gui.server

 
     It retrieves all that from a previously saved pickle file in /tmp."""
     # Called when tree has been deleted from memory.
-    tree_data = pickle.load(open(f'/tmp/{tid}.pickle', 'rb'))
+    try:
+        tree_data = pickle.load(open(f'/tmp/{tid}.pickle', 'rb'))
+    except (FileNotFoundError, EOFError, pickle.UnpicklingError) as e:
+        print(f'Tree {tid} cannot be recovered from disk. Loading placeholder.')
+        tree_data = TreeData()
+        tree_data.name = 'Placeholder tree'
+        tree_data.tree = Tree('(could,not,load,tree);')
+        ops.update_sizes_all(tree_data.tree)
+
     tree_data.style = copy_style(TreeStyle())
     tree_data.layouts = retrieve_layouts(tree_data.layouts)
     tree_data.active = drawer_module.get_empty_active()
     tree_data.timer = time()  # to track if it is active
+
     return tree_data
@@ -1634,7 +1643,12 @@

Source code for ete4.smartview.gui.server

         data.style = None  # since it can't be pickled
         data.layouts = layouts  # same
         data.active = None  # same
-        pickle.dump(data, open(f'/tmp/{tid}.pickle', 'wb'))
+        try:
+            pickle.dump(data, open(f'/tmp/{tid}.pickle', 'wb'))
+        except (pickle.PicklingError, PermissionError) as e:
+            print(f'Tree {tid} not saved to file.')
+            # So changing to ultrametric and back will not work,
+            # because it is done by re-reading from the dumped file.
     thr_write = Thread(daemon=True, target=write_tree_data)  # so we are not delayed
     thr_write.start()                                   # by big trees
 
diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html
index c71fc8e2..94b0cbb3 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 0x73cad0542a20> = 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 0x7f98a5d42a20> = 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/searchindex.js b/searchindex.js
index 1f795aa1..479c1a33 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", "reference/reference_smartview.rst", "reference/reference_taxonomy.rst", "reference/reference_tree.rst", "reference/reference_treematcher.rst", "reference/reference_treeview.rst", "tutorial/index.rst", "tutorial/tutorial_phylogeny.rst", "tutorial/tutorial_smartview.rst", "tutorial/tutorial_taxonomy.rst", "tutorial/tutorial_treematcher.rst", "tutorial/tutorial_trees.rst", "tutorial/tutorial_treeview.rst"], "titles": ["About", "Frequently Asked Questions", "Welcome to ETE\u2019s documentation!", "Reference Guide", "Clustering", "Tree operations", "Parsers", "Phylogenetic trees", "Multiple Sequence Alignments (SeqGroup)", "Smartview (web graphics)", "Taxonomy databases", "Tree (main class)", "Tree matcher", "Treeview (qt graphics)", "Tutorial", "Phylogenetic trees", "Tree drawing and exploration (web)", "Taxonomy databases", "Tree matcher", "Working with the Tree structure", "Tree drawing (Qt)"], "terms": {"The": [0, 1, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 20], "toolkit": [0, 17, 19, 20], "wa": [0, 5, 6, 19, 20], "origin": [0, 5, 7, 11, 15, 16, 17, 19, 20], "develop": 0, "bioinformat": [0, 7, 19], "depart": 0, "cipf": 0, "valencia": 0, "spain": 0, "greatli": 0, "improv": [0, 15], "compar": [0, 11, 14, 15], "genom": [0, 7, 9, 15, 17], "group": [0, 7, 10, 11, 15, 19], "crg": 0, "barcelona": 0, "structur": [0, 2, 4, 7, 11, 14, 15, 16, 18, 20], "comput": [0, 4, 9, 11, 19], "biologi": [0, 15], "unit": [0, 11, 20], "embl": 0, "heidelberg": 0, "germani": 0, "At": 0, "present": [0, 1, 7, 9, 10, 11, 15, 19], "i": [0, 4, 5, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "maintain": [0, 20], "metagenom": 0, "cbgp": 0, "madrid": 0, "citat": [0, 4, 7, 17], "3": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "reconstruct": 0, "analysi": [0, 4, 15, 16, 19, 20], "visual": [0, 2, 11, 14, 19], "phylogenom": 0, "data": [0, 4, 9, 11, 15, 16, 17, 19, 20], "jaim": 0, "huerta": [0, 7, 15], "cepa": [0, 7, 15], "francoi": 0, "serra": 0, "peer": 0, "bork": 0, "mol": 0, "biol": [0, 7], "evol": 0, "2016": 0, "doi": 0, "10": [0, 1, 8, 9, 16, 18, 19, 20], "1093": 0, "molbev": 0, "msw046": 0, "support": [0, 5, 6, 8, 9, 11, 18, 19], "etetoolkit": [0, 17], "googlegroup": 0, "com": [0, 11, 16, 17], "contact": 0, "jhcepa": [0, 11], "gmail": 0, "eggnog": 0, "orthologi": [0, 15], "databas": [0, 2, 3, 7, 14], "phylomedb": 0, "phylogenet": [0, 1, 2, 3, 5, 11, 14, 19], "polyphoni": 0, "3d": 0, "compars": 0, "phylemon": 0, "speci": [0, 1, 7, 10, 11, 14, 16, 18, 19, 20], "delimit": 0, "method": [0, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "treeko": [0, 7, 19], "duplic": [0, 1, 7, 11, 14], "awar": [0, 15], "tree": [0, 2, 3, 4, 6, 9, 10, 14], "agp": 0, "align": [0, 2, 3, 7, 9, 11, 14, 20], "free": [0, 18], "phylogeni": [0, 15], "itep": 0, "explor": [0, 1, 2, 9, 11, 14, 15, 19, 20], "microbi": 0, "pan": [0, 15, 17, 20], "t": [0, 1, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "rmsd": 0, "protein": [0, 9], "classif": [0, 17], "cansnper": 0, "genotyp": 0, "classifi": 0, "clonal": 0, "pathogen": 0, "reprophylo": 0, "reproduc": [0, 11, 20], "analys": [0, 15, 19, 20], "avocado": 0, "linux": 0, "autom": [0, 19], "test": [0, 14], "streptomedb": 0, "2": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "0": [0, 1, 4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "natur": [0, 19], "product": 0, "produc": [0, 5, 11, 18, 19], "streptomycet": 0, "iq": 0, "web": [0, 2, 3, 14, 17], "server": [0, 3, 11, 16, 17], "fast": [0, 19], "accur": 0, "under": [0, 4, 10, 11, 15, 16, 19], "maximum": [0, 8, 9, 19], "likelihood": 0, "A": [0, 1, 4, 5, 7, 10, 11, 12, 14, 16, 17, 19, 20], "brief": 0, "introduct": 0, "its": [0, 5, 6, 7, 9, 10, 11, 15, 16, 17, 19, 20], "programmat": 0, "featur": [0, 1, 4, 7, 11, 15, 16, 17, 19, 20], "scipi": 0, "confer": 0, "2015": 0, "littl": 0, "comparison": [0, 15, 19], "how": [0, 4, 11, 15, 16, 18, 20], "handl": [0, 19, 20], "r": [0, 6, 9, 15, 16, 19], "v": [0, 16, 20], "python": [0, 1, 11, 12, 15, 16, 18, 19, 20], "climateecologi": 0, "blog": 0, "sever": [0, 1, 11, 15, 16, 17, 18, 19, 20], "wai": [0, 1, 11, 15, 17, 18, 19, 20], "displai": 0, "associ": [0, 4, 7, 8, 10, 11, 15, 17], "bacpathgenom": 0, "pars": [0, 4, 7, 10, 11, 15, 17, 19], "list": [0, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 20], "word": [0, 10, 15, 19], "build": [0, 9], "trie": 0, "stackoverflow": 0, "annot": [0, 7, 10, 14], "holt": 0, "lab": 0, "script": [0, 1, 17], "guid": [0, 2], "ete3": [0, 16], "api": [0, 9], "exampl": [0, 1, 4, 5, 6, 7, 8, 9, 11, 14, 15, 17, 19, 20], "e": [0, 1, 5, 9, 10, 11, 16, 18, 19, 20], "noutahi": 0, "plot": [0, 20], "avrilom": 0, "includ": [1, 5, 7, 8, 15, 16, 17, 18, 19, 20], "basic": [1, 7, 14, 15, 16, 20], "standalon": [1, 15], "program": [1, 16, 18, 19, 20], "quickli": [1, 18, 19], "your": [1, 15, 16, 17, 19], "type": [1, 9, 11, 15, 16, 19, 20], "ete4": [1, 9, 11, 14, 15, 16, 18, 19, 20], "file": [1, 4, 6, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "termin": [1, 11, 15, 16, 19, 20], "run": [1, 16, 18], "For": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "instanc": [1, 7, 10, 11, 15, 16, 17, 19, 20], "mytreefil": 1, "nw": [1, 4, 9, 11, 15, 16, 19, 20], "simpl": [1, 4, 14, 15, 17, 19, 20], "implement": [1, 7, 19, 20], "doe": [1, 10, 12, 15, 17, 18, 19, 20], "allow": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "fanci": 1, "custom": [1, 10, 11, 14, 17], "howev": [1, 15, 17, 19, 20], "more": [1, 5, 7, 11, 15, 16, 18, 19, 20], "than": [1, 5, 11, 15, 16, 17, 19, 20], "main": [1, 2, 3, 9, 16, 17, 18, 19, 20], "goal": 1, "provid": [1, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "librari": 1, "so": [1, 5, 7, 11, 16, 17, 18, 19], "you": [1, 7, 8, 15, 16, 17, 19, 20], "creat": [1, 4, 5, 9, 11, 12, 15, 16], "own": [1, 15, 16, 19, 20], "manipul": [1, 16, 19, 20], "shell": 1, "could": [1, 4, 11, 15, 16, 18, 19, 20], "from": [1, 5, 6, 7, 9, 10, 11, 14, 15, 16, 17, 20], "import": [1, 5, 11, 15, 16, 17, 18, 19, 20], "t1": [1, 4, 11, 19], "b": [1, 4, 5, 11, 16, 17, 18, 19, 20], "c": [1, 4, 5, 11, 16, 18, 19, 20], "string": [1, 4, 7, 8, 11, 12, 15, 19], "t2": [1, 4, 11, 15, 19], "open": [1, 4, 9, 10, 11, 16, 19], "mani": [1, 7, 9, 11, 15, 19, 20], "tutori": [1, 2], "follow": [1, 4, 7, 11, 15, 16, 17, 19, 20], "shortcut": [1, 16, 18], "note": [1, 7, 11, 15, 16, 17, 18, 19, 20], "assum": [1, 7, 19], "tip1": 1, "There": [1, 11, 15, 18, 19, 20], "thi": [1, 4, 5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "easiest": [1, 17], "one": [1, 4, 7, 9, 11, 15, 16, 17, 18, 19, 20], "travers": [1, 3, 5, 11, 14, 18, 20], "print": [1, 5, 8, 11, 15, 16, 17, 18, 19], "ye": [1, 15, 18], "current": [1, 5, 7, 8, 9, 10, 11, 15, 16, 19], "strategi": [1, 11, 12, 17, 19], "pre": [1, 5, 10, 11, 16, 19, 20], "post": [1, 5, 9, 11, 19], "level": [1, 5, 10, 11, 15, 16, 19], "over": [1, 7, 8, 11, 15, 18, 19, 20], "check": [1, 11, 14, 15, 16, 18, 20], "differ": [1, 7, 9, 11, 14, 15, 16, 18, 19, 20], "http": [1, 11, 16, 17, 19], "packag": [1, 15, 17], "org": [1, 11, 19], "tutorial_tre": 1, "html": [1, 9], "slightli": [1, 19], "across": 1, "subformat": 1, "label": [1, 7, 9, 15, 16, 17, 19, 20], "descript": [1, 4, 9, 11, 16, 19, 20], "flexibl": [1, 19], "d": [1, 4, 5, 7, 9, 11, 15, 16, 18, 19, 20], "7": [1, 9, 11, 16, 19], "f": [1, 5, 11, 15, 16, 18, 19, 20], "5": [1, 4, 9, 11, 15, 16, 18, 19, 20], "1": [1, 4, 5, 6, 7, 9, 10, 11, 12, 15, 17, 18, 19, 20], "6": [1, 7, 9, 11, 16, 19, 20], "h": [1, 7, 11, 15, 16, 18, 19, 20], "8": [1, 7, 9, 11, 16, 19, 20], "w": [1, 11, 16, 19, 20], "length": [1, 6, 9, 11, 15, 19], "4": [1, 9, 11, 15, 18, 19, 20], "leav": [1, 4, 5, 7, 9, 11, 15, 16, 17, 18, 20], "onli": [1, 5, 7, 9, 11, 14, 15, 16, 17, 19, 20], "9": [1, 9, 10, 11, 15, 16, 19], "100": [1, 11, 16, 19, 20], "topologi": [1, 5, 7, 11, 14, 15, 16, 20], "In": [1, 11, 15, 16, 17, 18, 19, 20], "specifi": [1, 4, 9, 11, 15, 19], "parser": [1, 2, 3, 4, 7, 9, 11, 12, 15, 18, 19], "my_tre": 1, "when": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "default": [1, 4, 6, 7, 11, 15, 16, 17, 19, 20], "": [1, 4, 6, 7, 9, 10, 11, 12, 15, 18, 20], "distanc": [1, 4, 5, 9, 11, 14, 15], "depend": [1, 5, 11, 15, 19, 20], "If": [1, 5, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "want": [1, 5, 11, 16, 18, 19, 20], "save": [1, 9, 15, 16, 19, 20], "other": [1, 5, 7, 11, 12, 15, 16, 17, 19, 20], "properti": [1, 4, 5, 6, 7, 9, 10, 11, 14, 15, 17], "need": [1, 6, 9, 10, 12, 15, 16, 19, 20], "them": [1, 5, 8, 10, 11, 15, 16, 18, 19, 20], "call": [1, 9, 11, 12, 15, 16, 17, 18, 19, 20], "prop": [1, 5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "size": [1, 5, 7, 9, 10, 11, 16, 19, 20], "none": [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "start": [1, 5, 6, 9, 11, 16, 18, 19, 20], "version": [1, 7, 9, 12, 15, 17, 19], "render": [1, 3, 11, 14, 15, 16], "mode": [1, 20], "automat": [1, 7, 9, 11, 14, 18, 19, 20], "detect": [1, 7, 11, 14, 17, 19], "filenam": [1, 9], "extens": [1, 11, 15, 20], "code": [1, 5, 7, 9, 11, 12, 15, 16, 17, 19, 20], "vector": [1, 20], "mytre": [1, 20], "chang": [1, 5, 6, 11, 15, 16, 18, 19], "layout": [1, 11, 14, 15], "By": [1, 4, 7, 15, 16, 19], "function": [1, 4, 5, 7, 9, 11, 15, 17, 18], "abl": [1, 16, 18, 19], "add": [1, 4, 5, 7, 8, 9, 10, 11, 17, 19], "remov": [1, 3, 5, 9, 11], "modifi": [1, 14, 16, 20], "almost": 1, "ani": [1, 5, 6, 9, 10, 11, 15, 16, 17, 18, 19, 20], "element": [1, 9, 11, 16, 19, 20], "face": [1, 3, 11, 14], "attrfac": [1, 9, 20], "treestyl": [1, 3, 11, 15, 16, 20], "def": [1, 7, 15, 16, 19, 20], "my_layout": 1, "is_leaf": [1, 6, 11, 16, 18, 19, 20], "name_fac": 1, "els": [1, 16, 17, 19, 20], "fsize": [1, 20], "small": [1, 16, 19, 20], "font": 1, "prefer": [1, 9, 15], "posit": [1, 5, 6, 11, 18, 19], "add_face_to_nod": [1, 20], "column": [1, 9, 11, 16, 20], "right": [1, 9, 11, 16, 19, 20], "show_leaf_nam": [1, 11, 16, 20], "fals": [1, 5, 7, 9, 10, 11, 12, 15, 16, 19, 20], "again": [1, 15, 18, 19], "layout_fn": [1, 20], "g": [1, 6, 11, 16, 18, 19, 20], "m1_t1": 1, "m_1_t2": 1, "m2_t3": 1, "m2_t1": 1, "m2_t2": 1, "show": [1, 9, 11, 15, 19], "tree_styl": [1, 9, 11, 15, 16, 20], "style": [1, 9, 11, 14], "experi": 1, "extrem": 1, "convert": [1, 5, 7, 10, 11, 15, 17, 19], "ultrametr": [1, 5, 9, 11, 16], "make": [1, 5, 11, 16, 17, 18, 19, 20], "end": [1, 6, 9, 11, 16, 18, 19, 20], "same": [1, 7, 9, 11, 15, 16, 17, 18, 19, 20], "popul": [1, 3, 5, 11, 16, 19, 20], "50": [1, 6, 16, 19, 20], "random_branch": [1, 16, 20], "true": [1, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 19, 20], "to_ultrametr": [1, 3, 5, 11], "enabl": [1, 16], "force_topologi": 1, "option": [1, 7, 12, 16, 18, 19, 20], "seen": [1, 7, 11, 19], "engin": [1, 15, 16, 20], "case": [1, 11, 15, 16, 19, 20], "actual": [1, 19], "about": [2, 7, 9, 15, 16, 18, 19, 20], "highlight": [2, 16, 20], "tool": [2, 19], "us": [2, 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 19, 20], "relat": [2, 5, 11, 17, 18, 19], "link": [2, 4, 7, 14, 16, 19, 20], "resourc": [2, 17], "work": [2, 7, 14, 20], "draw": [2, 11, 14, 15], "qt": [2, 3, 14], "taxonomi": [2, 3, 7, 14], "matcher": [2, 3, 14], "refer": [2, 5, 7, 11, 15, 16, 17, 19, 20], "class": [2, 3, 4, 5, 7, 8, 9, 10, 12, 15, 16, 17, 18, 19, 20], "oper": [2, 3, 8, 11, 14, 20], "cluster": [2, 3, 19], "multipl": [2, 3, 7, 14, 17], "sequenc": [2, 3, 5, 7, 9, 11, 14], "seqgroup": [2, 3, 15], "smartview": [2, 3, 11, 16], "graphic": [2, 3, 4, 16, 19, 20], "treeview": [2, 3, 20], "frequent": [2, 19], "ask": [2, 15], "question": 2, "gener": [2, 5, 11, 15, 16, 19, 20], "brows": [2, 14], "read": [2, 6, 7, 9, 14, 15, 16, 20], "write": [2, 7, 8, 11, 14, 15, 16, 18], "index": [2, 4, 5], "modul": [2, 8, 9, 12, 16, 17, 18, 19, 20], "search": [2, 3, 5, 9, 11, 12, 18], "page": [2, 15, 16, 20], "walker": [3, 5], "add_branch_valu": [3, 5], "add_leaf_nam": [3, 5], "assert_root_consist": [3, 5], "common_ancestor": [3, 5, 11, 15, 16, 19, 20], "create_dichotomic_sist": [3, 5], "farthest": [3, 5, 7, 11, 15, 19], "farthest_descend": [3, 5], "insert_intermedi": [3, 5], "interchange_refer": [3, 5], "join_branch": [3, 5], "ladder": [3, 5, 11], "make_nam": [3, 5, 9], "midpoint": [3, 5, 14], "move": [3, 5], "populate_uniform": [3, 5], "populate_yul": [3, 5], "rehang": [3, 5], "resolve_polytomi": [3, 5, 11, 19], "root_at": [3, 5], "set_midpoint_outgroup": [3, 5], "set_outgroup": [3, 5, 11, 19], "sort": [3, 5, 9, 10, 11, 20], "swap_prop": [3, 5], "to_dendrogram": [3, 5], "traverse_bf": [3, 5], "unroot": [3, 5, 11], "update_s": [3, 5], "update_sizes_al": [3, 5], "update_sizes_from": [3, 5], "walk": [3, 5], "newick": [3, 4, 7, 9, 11, 12, 14, 15, 16, 17, 18], "nexu": 3, "phylotre": [3, 10, 15, 17, 18, 19], "evolev": [3, 15], "clustertre": [3, 4], "ncbitaxa": [3, 17], "gtdbtaxa": [3, 17], "nodestyl": [3, 16, 20], "treepattern": [3, 12, 18], "match": [3, 4, 7, 9, 10, 11, 12, 15, 18], "safer_ev": [3, 9, 12], "children": [4, 5, 7, 9, 11, 12, 16, 18, 19, 20], "text_arrai": 4, "fdist": 4, "spearman_dist": 4, "sourc": [4, 6, 7, 8, 9, 10, 12, 16, 19, 20], "base": [4, 7, 9, 11, 15, 17, 19, 20], "repres": [4, 5, 6, 9, 10, 11, 15, 16, 17, 19, 20], "result": [4, 5, 8, 9, 10, 11, 15, 18, 19], "__init__": [4, 7, 8, 9, 10, 11, 12, 16, 20], "paramet": [4, 5, 7, 8, 9, 10, 11, 12, 16, 20], "object": [4, 6, 7, 9, 11, 19, 20], "dict": [4, 6, 9, 10, 11, 16], "content": [4, 6, 7, 11, 14], "singl": [4, 7, 10, 11, 15, 16, 19, 20], "node": [4, 5, 6, 7, 9, 10, 11, 12, 14, 17], "It": [4, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "can": [4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "number": [4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "format": [4, 6, 7, 8, 9, 10, 11, 15, 17, 19, 20], "fine": [4, 11], "grain": [4, 11], "interpret": [4, 9, 11, 15, 16, 19], "see": [4, 7, 9, 11, 15, 16, 18, 19, 20], "pyx": [4, 11], "empti": [4, 11, 15, 17, 19, 20], "name": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 17, 18, 19], "t3": [4, 11, 19], "t4": [4, 11], "home": [4, 11], "user": [4, 11, 16, 17, 19, 20], "my": [4, 11, 16, 20], "deviat": 4, "get_dunn": 4, "calcul": [4, 7, 10, 11, 15, 19], "dunn": 4, "given": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 20], "set": [4, 5, 7, 8, 9, 10, 11, 14, 15, 16, 19, 20], "descend": [4, 5, 7, 10, 11, 14, 16, 18], "get_silhouett": 4, "silhouett": 4, "valu": [4, 5, 7, 9, 11, 15, 16, 17, 18, 19, 20], "euclidean": 4, "also": [4, 7, 9, 10, 11, 15, 17, 18, 19, 20], "profil": [4, 20], "mean": [4, 15, 16, 20], "inter": 4, "intra": 4, "analyz": [4, 19], "intraclust": 4, "interclust": 4, "silhouet": 4, "ar": [4, 7, 8, 10, 11, 12, 15, 16, 17, 18, 19, 20], "centroid": 4, "diamet": [4, 5, 16, 20], "linkag": 4, "rousseeuw": 4, "p": [4, 15, 16, 18, 19], "j": [4, 7, 11, 18, 19], "1987": 4, "aid": 4, "valid": [4, 5, 7, 9, 10, 11, 19], "appl": 4, "math": [4, 16], "20": [4, 9, 16, 20], "53": 4, "65": [4, 16, 20], "intercluster_dist": 4, "intracluster_dist": 4, "leaf_profil": 4, "yield": [4, 5, 9, 11, 12, 18, 19], "link_to_arrayt": 4, "arraytbl": 4, "arrayt": 4, "return": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19, 20], "been": [4, 15], "found": [4, 7, 15, 16, 18, 19, 20], "row": [4, 9, 11], "expect": [4, 7, 15, 18, 19], "leaf": [4, 5, 6, 7, 9, 10, 11, 15, 17, 18, 19], "set_distance_funct": 4, "fn": [4, 7], "silouett": 4, "acept": 4, "two": [4, 5, 11, 15, 16, 18, 19, 20], "numpi": [4, 16], "arrai": [4, 9, 11, 16], "argument": [4, 6, 7, 10, 15, 16, 19, 20], "my_dist_fn": 4, "lambda": [4, 11, 15, 17, 19], "x": [4, 6, 9, 11, 16, 18], "y": [4, 6, 9, 11, 16, 18, 19], "ab": [4, 16, 19], "root": [5, 7, 11, 14, 16, 17, 18, 20], "branch": [5, 9, 10, 11, 14, 15], "prun": 5, "add_next_branch": 5, "self": [5, 7, 9, 11, 16, 19, 20], "first_visit": 5, "go_back": 5, "has_unvisited_branch": 5, "node_id": [5, 9, 11], "dist_fn": [5, 11], "support_fn": [5, 11], "bprop": [5, 11], "rais": [5, 11, 19], "assertionerror": 5, "look": [5, 18, 19], "inconsist": 5, "last": [5, 9, 11, 19], "common": [5, 7, 9, 10, 11, 15, 16, 18, 20], "lineag": [5, 7, 10, 11, 15, 17], "don": 5, "have": [5, 10, 11, 15, 16, 18, 19], "ancestor": [5, 9, 10, 11, 16], "whose": [5, 16, 19, 20], "we": [5, 9, 11, 15, 16, 17, 18, 19, 20], "find": [5, 11, 15, 16, 18], "dichotomi": 5, "old": [5, 11], "new": [5, 7, 9, 11, 15, 16, 18, 19], "sister": [5, 11, 19], "topolog": [5, 7, 11, 15, 18, 19], "intermedi": [5, 11, 17], "dist": [5, 6, 9, 11, 16, 18, 19, 20], "insert": 5, "between": [5, 7, 11, 14, 15, 16], "parent": [5, 9, 10, 11, 16, 18, 19], "an": [5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "node1": [5, 11, 19], "node2": [5, 11, 19], "interchang": 5, "point": [5, 9, 11, 15, 17, 19], "where": [5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "viceversa": 5, "substitut": [5, 15, 18], "child": [5, 7, 10, 11, 19], "revers": [5, 9, 11], "accord": [5, 6, 7, 9, 11, 15, 19, 20], "each": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "partit": [5, 7, 11, 15, 19], "instead": [5, 11, 18, 19, 20], "sum": [5, 11, 19], "lenght": [5, 11, 19], "biggest": 5, "first": [5, 7, 9, 10, 11, 15, 16, 17, 18, 20], "char": [5, 8], "abcdefghijklmnopqrstuvwxyz": 5, "short": [5, 11, 18], "correspond": [5, 6, 7, 9, 10, 15, 18, 19, 20], "middl": 5, "exact": [5, 10, 15, 19], "center": [5, 9, 20], "shift": 5, "respect": [5, 19], "model": [5, 11], "yule": [5, 11], "dichotom": [5, 11], "random": [5, 11, 16, 19, 20], "all": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 20], "necessari": [5, 11, 15, 17, 19], "too": [5, 7, 11, 12, 19], "collect": [5, 8, 11, 16, 19, 20], "letter": [5, 7, 11, 15], "hard": [5, 11], "everi": [5, 9, 11, 15, 16, 19], "step": [5, 11, 17, 19], "randomli": [5, 7, 11], "select": [5, 9, 11, 19], "grow": [5, 11, 19], "uniform": [5, 11], "pda": [5, 11], "interior": [5, 11], "newli": [5, 11], "intern": [5, 7, 9, 10, 11, 15, 17, 19, 20], "child_po": 5, "seri": [5, 9, 11], "dicotomi": [5, 11], "polytomi": [5, 11, 19], "ha": [5, 6, 9, 11, 15, 16, 18, 19], "dicotom": [5, 11], "modif": [5, 11, 20], "arbitrari": [5, 11, 18, 20], "should": [5, 7, 11, 12, 15, 16, 19, 20], "resolv": [5, 11], "otherwis": [5, 10, 11, 15, 16], "do": [5, 11, 12, 15, 16, 18, 19, 20], "still": [5, 11], "Its": [5, 7, 19], "lost": [5, 19], "outgroup": [5, 11, 14], "futur": [5, 11, 17], "put": [5, 9, 11, 16], "kei": [5, 7, 17, 19], "place": [5, 11, 12, 15, 19, 20], "n1": [5, 16, 19, 20], "n2": [5, 16, 19, 20], "swap": 5, "dendrogram": 5, "equidist": [5, 11, 16], "order": [5, 11, 15, 16, 17, 19, 20], "is_leaf_fn": [5, 6, 7, 11, 19], "breadth": [5, 11], "convent": [5, 11, 19], "real": [5, 11, 15, 20], "typic": [5, 11], "just": [5, 11, 15, 18, 19], "hang": [5, 11, 19], "updat": [5, 8, 9, 10, 11, 15, 17], "iter": [5, 7, 8, 11, 18], "except": [6, 18, 19], "newickerror": 6, "content_repr": 6, "dump": [6, 10, 15, 17], "fp": 6, "format_root_nod": [6, 7, 11], "represent": [6, 7, 8, 9, 11, 16, 19, 20], "error": [6, 9, 11, 18], "text": [6, 8, 9, 11, 15, 16, 17, 19, 20], "get_extended_prop": 6, "extract": [6, 9, 17], "nhx": [6, 15, 19], "foo": 6, "bar": [6, 9], "get_prop": [6, 11], "abc": 6, "123": 6, "load": [6, 9, 11, 15, 17, 19, 20], "tree_text": 6, "tree_class": 6, "make_pars": 6, "int": [6, 9, 20], "prop_repr": 6, "accept": [6, 11, 16, 17, 18, 19, 20], "quot": [6, 16, 18], "escaped_char": 6, "n": [6, 8, 9, 11, 15, 16, 18, 19, 20], "charact": [6, 15], "escap": 6, "read_cont": 6, "unicod": 6, "po": [6, 9], "u": [6, 16, 19, 20], "read_nod": 6, "nodes_text": 6, "thei": [6, 7, 11, 15, 16, 17, 19, 20], "repr_short": 6, "obj": 6, "max_len": 6, "limit": [6, 9, 15, 18, 19, 20], "skip_quoted_nam": 6, "skip_spaces_and_com": 6, "after": [6, 7, 11, 15, 16, 19, 20], "whitespac": 6, "comment": [6, 8], "unquot": 6, "nexuserror": 6, "apply_transl": 6, "translat": [6, 7, 10, 15, 17], "get_command": 6, "text_sect": 6, "command": [6, 9, 16, 19], "get_sect": 6, "section_nam": 6, "arg": [6, 9, 20], "section": [6, 16, 19], "full": [6, 11, 15, 16, 19], "get_tre": 6, "transform": 6, "done": [6, 15, 16, 19], "alg_format": [7, 15], "fasta": [7, 8, 15, 16], "sp_naming_funct": [7, 15, 17], "store": [7, 8, 9, 11, 12, 15, 16, 17, 19], "extend": [7, 9, 11, 15, 19], "standard": [7, 11, 19, 20], "ad": [7, 10, 11, 14, 16, 17, 19, 20], "specif": [7, 16, 17, 19, 20], "phylogent": 7, "initi": [7, 9, 15, 16, 20], "which": [7, 11, 15, 16, 17, 19, 20], "contain": [7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "phylip": [7, 8], "iphylip": [7, 8, 15], "interleav": [7, 8], "get": [7, 9, 10, 14, 15, 16, 18], "set_species_naming_funct": [7, 15], "identifi": [7, 9, 15, 17], "annotate_gtdb_taxa": [7, 17], "taxid_attr": [7, 10, 17], "tax2nam": [7, 10, 17], "tax2track": [7, 10, 17], "tax2rank": [7, 10, 17], "dbfile": [7, 10], "annotate_ncbi_taxa": [7, 17], "ncbi": [7, 10, 14], "encod": [7, 8, 11, 15, 19], "taxid": [7, 9, 10, 14], "spname": 7, "scientif": [7, 9, 10, 17, 20], "spci": 7, "named_lineag": [7, 10, 17], "track": [7, 10, 17], "inform": [7, 9, 11, 14, 16, 19, 20], "access": [7, 15, 16, 17, 19, 20], "dictionari": [7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "avoid": [7, 8, 16, 19], "queri": [7, 16, 17, 19], "rank": [7, 10, 17], "param": 7, "local": [7, 10, 14, 16, 18], "copi": [7, 11, 14, 20], "tax2lineag": [7, 17], "collapse_lineage_specific_expans": [7, 15], "return_copi": 7, "expans": [7, 15], "tip": [7, 9, 11, 18, 19], "chosen": 7, "within": [7, 9, 11, 14, 15, 16, 17], "suppli": [7, 11], "criteria": [7, 11], "prune": [7, 9, 10, 11, 14, 15, 16, 17], "process": [7, 9, 15, 17, 19], "get_ag": [7, 15], "species2ag": [7, 15], "phylostratigraf": 7, "describ": [7, 11, 15, 16, 18], "gabaldon": [7, 15], "2011": [7, 15], "assign": [7, 9, 11, 15, 17], "event": [7, 9, 14], "rel": [7, 11, 14, 18], "tempor": [7, 15], "scale": [7, 9, 15, 16], "wide": [7, 15, 19], "studi": [7, 15], "27": [7, 16], "38": 7, "45": [7, 16, 17, 20], "get_age_balanced_outgroup": 7, "better": [7, 19], "balanc": [7, 11, 19], "ag": [7, 15], "get_descendant_evol_ev": [7, 15], "sos_thr": [7, 15], "speciat": [7, 15, 19], "overlap": [7, 16, 19], "linag": [7, 17], "detail": [7, 19, 20], "human": [7, 9, 11, 15, 19, 20], "phylom": 7, "dopazo": 7, "2007": [7, 15], "r109": 7, "get_farthest_oldest_leaf": [7, 15], "oldest": [7, 15], "requir": [7, 10, 11, 15, 17, 18, 19, 20], "estim": [7, 20], "pointer": [7, 19, 20], "receiv": [7, 11, 20], "uniqu": [7, 9, 11, 17], "dynam": [7, 11, 15, 16, 19, 20], "collaps": [7, 9, 10, 11], "get_farthest_oldest_nod": [7, 15], "seq": [7, 8, 16, 20], "get_my_evol_ev": [7, 15], "involv": [7, 15, 19], "scan": [7, 15], "dup": [7, 15], "algorithm": [7, 16, 19], "leafnam": 7, "get_speciation_tre": [7, 15], "map_properti": 7, "autodetect_dupl": [7, 15], "newick_onli": [7, 15], "possibl": [7, 9, 11, 15, 19, 20], "gene": [7, 9, 11, 14], "famili": [7, 11, 14, 17, 20], "marcet": [7, 15], "map": [7, 11, 15, 16], "subtre": [7, 9, 12, 16, 18, 19, 20], "get_descendants_evol_ev": 7, "evoltyp": [7, 15], "get_speci": [7, 15], "cover": 7, "iter_speci": 7, "link_to_align": [7, 15], "kwarg": [7, 8, 9], "ncbi_compar": 7, "cached_cont": [7, 11], "reconcil": [7, 15], "species_tre": 7, "reconcili": 7, "evolutionari": [7, 9, 14, 19], "infer": [7, 15, 17, 19], "take": [7, 15, 17, 18, 19], "nodenam": 7, "parse_sp_nam": 7, "node_nam": 7, "split": [7, 17, 19], "_": [7, 15, 19], "split_by_dup": [7, 15], "outfil": [7, 8, 11, 19], "str": [7, 9, 11], "output": [7, 8, 11, 15, 16, 18], "instad": [7, 11], "avail": [7, 9, 11, 15, 16, 19, 20], "bool": [7, 9, 11], "compat": [7, 11, 19], "reason": [7, 11, 15, 18, 19], "sci_nam": [7, 9, 10, 11, 17], "ocur": 7, "etyp": [7, 15], "l": [7, 15, 19, 20], "loss": [7, 15], "in_seq": [7, 15], "side": [7, 11, 16], "out_seq": [7, 15], "sequenci": 8, "fix_dupl": 8, "path": [8, 11, 15, 19, 20], "altern": [8, 10, 15, 19], "forc": 8, "To": [8, 11, 15, 16, 17, 19, 20], "effect": [8, 11], "relax": 8, "phylip_relax": 8, "iphylip_relax": 8, "seqs_str": 8, "seq1": 8, "aaaaaaaaaaa": 8, "seq2": 8, "ttttttttttttt": 8, "get_seq": [8, 9, 16], "get_entri": 8, "entri": 8, "iter_entri": 8, "item": [8, 9, 10, 11, 17, 19, 20], "tupl": [8, 9, 11, 20], "set_seq": 8, "written": [8, 20], "keep": [9, 10, 11, 15, 16, 19, 20], "rest": [9, 19, 20], "talk": 9, "world": 9, "id": [9, 11, 16, 19], "delet": [9, 11], "globalstuff": 9, "treedata": 9, "core": [9, 11, 15], "include_prop": [9, 11, 16], "exclude_prop": [9, 11, 16], "timer": 9, "float": [9, 11, 16, 20], "activ": [9, 16], "namedtupl": 9, "0x73cad0542a20": 9, "activate_clad": 9, "tree_id": 9, "activate_nod": 9, "add_tre": 9, "add_trees_from_request": 9, "app": 9, "callback": 9, "change_selection_nam": 9, "tid": 9, "copy_styl": 9, "deactivate_clad": 9, "deactivate_nod": 9, "del_tre": 9, "everywher": 9, "appear": [9, 11, 15, 16, 19], "referenc": 9, "find_nod": 9, "get_active_clad": 9, "get_command_search": 9, "appropri": [9, 12, 15], "get_draw": 9, "get_eval_search": 9, "express": [9, 12, 14], "evalu": [9, 16, 18], "get_layout": 9, "get_layouts_from_gett": 9, "layout1": 9, "submodul": 9, "get_newick": 9, "max_mb": 9, "get_next_available_port": 9, "host": [9, 11], "localhost": [9, 11, 16], "port_min": 9, "5000": [9, 11, 16], "port_max": 9, "6000": 9, "next": [9, 11, 19, 20], "port": [9, 11], "socket": 9, "get_nodes_info": 9, "get_par": 9, "count_leav": 9, "get_pars": 9, "get_search_funct": 9, "get_selection_info": 9, "tree_data": 9, "info": [9, 11, 20], "get_select": 9, "get_stat": 9, "pname": 9, "some": [9, 15, 16, 17, 19, 20], "statist": 9, "get_tid": 9, "get_topological_search": 9, "pattern": [9, 12, 18, 19], "get_trees_from_fil": 9, "fileobject": 9, "get_trees_from_form": 9, "form": [9, 11, 16], "request": [9, 11], "get_trees_from_nexus_or_newick": 9, "btext": 9, "name_newick": 9, "safe_mod": 9, "compress": [9, 11], "global": 9, "initialize_tree_styl": 9, "json_error": 9, "load_tre": 9, "load_tree_from_newick": 9, "memori": [9, 10, 19], "mainten": 9, "check_interv": 9, "60": [9, 16, 20], "max_tim": 9, "1800": 9, "perform": [9, 15, 16, 19, 20], "task": [9, 19], "second": [9, 15, 18, 19], "like": [9, 11, 16, 17, 18, 19], "nice_html": 9, "titl": [9, 16], "open_browser_window": 9, "try": [9, 18], "browser": [9, 16], "window": 9, "prune_by_select": 9, "remove_act": 9, "idx": 9, "remove_active_clad": 9, "remove_search": 9, "remove_select": 9, "req_json": 9, "what": [9, 12, 16, 18, 19], "json": 9, "would": [9, 15, 18, 19], "gracefulli": 9, "abort": 9, "retrieve_layout": 9, "retrieve_tree_data": 9, "retriev": [9, 15, 17, 19], "previous": [9, 15, 19, 20], "pickl": [9, 19], "tmp": 9, "run_smartview": 9, "quiet": [9, 11, 16], "keep_serv": [9, 11, 16], "open_brows": [9, 11], "safer": [9, 12], "eval": [9, 12, 16], "search_to_select": 9, "key_text": 9, "sub": [9, 10, 18, 19], "store_act": 9, "store_search": 9, "store_select": 9, "touch_and_get": 9, "unselect_nod": 9, "update_app_available_layout": 9, "update_layout": 9, "active_layout": 9, "front": [9, 11], "statu": 9, "update_node_prop": 9, "update_node_styl": 9, "update_select": 9, "alia": 9, "field": [9, 16], "viewport": 9, "panel": 9, "zoom": [9, 16], "collapsed_id": [9, 16], "subclass": 9, "extra": [9, 16, 18, 19, 20], "collapse_s": [9, 16], "min_siz": [9, 16], "npanel": 9, "draw_aligned_head": 9, "draw_collaps": 9, "collapsed_nod": 9, "active_children": 9, "selected_children": 9, "draw_cont": 9, "draw_nod": 9, "bdx": 9, "bdy": 9, "bdy0": 9, "bdy1": 9, "flush_outlin": 9, "minimum_dx": 9, "box": [9, 16], "outlin": 9, "reset": 9, "get_active_children": 9, "get_collapsed_nod": 9, "either": [9, 17, 19], "get_outlin": 9, "get_popup_prop": 9, "safe": [9, 19], "popup": [9, 11], "get_selected_children": 9, "is_fully_collaps": 9, "utterli": 9, "width": [9, 11, 16, 20], "on_first_visit": 9, "on_last_visit": 9, "draweraligncircfac": 9, "draweralignrectfac": 9, "drawercirc": 9, "minim": [9, 10], "circular": [9, 16, 19], "circ": 9, "content_s": 9, "draw_childrenlin": 9, "p1": 9, "p2": 9, "arc": 9, "span": 9, "draw_lengthlin": 9, "parent_of": 9, "line": [9, 11, 16, 19, 20], "draw_nodebox": 9, "searched_bi": 9, "draw_nodedot": 9, "max_siz": 9, "active_nod": 9, "minimum_dr": 9, "get_box": 9, "in_viewport": 9, "is_smal": 9, "node_s": 9, "drawercircfac": 9, "bdr": 9, "bda": 9, "bda0": 9, "bda1": 9, "drawerrect": 9, "rectangular": [9, 16, 20], "rect": [9, 20], "circl": [9, 16, 20], "squar": [9, 16], "sm_style": [9, 11, 16], "drawerrectfac": 9, "dx": [9, 16], "dy": [9, 16], "treeactiv": 9, "clade": [9, 17], "drawn_siz": 9, "min_x": 9, "get_asec": 9, "annular": 9, "sector": 9, "get_empty_act": 9, "get_rect": 9, "rectangl": [9, 16], "make_box": 9, "safe_str": 9, "stack": 9, "box1": 9, "box2": 9, "pad": [9, 11, 16], "cartesian": 9, "circumasec": 9, "circumscrib": 9, "circumrect": 9, "asec": 9, "clip_angl": 9, "a1": [9, 16, 20], "a2": [9, 16, 20], "angl": 9, "pi": 9, "draw_arc": 9, "larg": [9, 11, 16, 19], "arc_typ": 9, "draw_arrai": 9, "tooltip": [9, 16], "draw_arrow": 9, "orient": 9, "arrow_typ": 9, "arrow": 9, "bound": 9, "draw_circl": 9, "radiu": [9, 20], "circle_typ": 9, "draw_ellips": 9, "rx": 9, "ry": 9, "ellipse_typ": 9, "draw_html": 9, "html_type": 9, "draw_img": 9, "img": 9, "img_typ": 9, "draw_lin": 9, "line_typ": 9, "draw_outlin": 9, "draw_rect": 9, "rect_typ": 9, "draw_rhombu": 9, "rhombus_typ": 9, "rhombu": 9, "draw_slic": 9, "da": 9, "slice_typ": 9, "draw_text": [9, 16], "text_typ": 9, "rotat": [9, 16], "anchor": 9, "draw_triangl": 9, "triangle_typ": 9, "triangl": [9, 16], "defin": [9, 15, 17, 18, 19, 20], "top": [9, 11, 16, 19, 20], "left": [9, 16, 19], "first_valu": 9, "get_line_typ": 9, "get_x": 9, "get_i": 9, "intersects_angl": 9, "part": [9, 15, 17, 18, 19, 20], "intersects_box": 9, "b1": [9, 16, 20], "b2": [9, 16, 20], "kind": [9, 18, 19], "intersect": 9, "intersects_seg": 9, "s1": 9, "s2": 9, "segment": 9, "split_thru_negative_xaxi": 9, "cut": [9, 11, 19], "summari": 9, "summar": 9, "alignlinkfac": 9, "stroke_color": 9, "grai": [9, 16, 20], "stroke_width": 9, "opac": [9, 16, 20], "solid": [9, 16, 20], "dot": [9, 11, 16, 20], "dash": [9, 16, 20], "compute_bounding_box": 9, "dx_to_closest_child": 9, "n_row": 9, "n_col": 9, "dx_befor": 9, "dy_befor": 9, "fit": 9, "overriden": 9, "inherit": [9, 16], "alignmentfac": [9, 16], "seqtyp": [9, 16], "aa": [9, 16, 19], "gap_format": [9, 16, 20], "seq_format": [9, 16, 20], "height": [9, 11, 16, 19, 20], "fgcolor": [9, 16, 20], "black": [9, 16, 19, 20], "bgcolor": [9, 16, 20], "bcc3d0": [9, 16], "gapcolor": [9, 16, 20], "gap_linewidth": [9, 16], "max_fsiz": [9, 16], "12": [9, 16, 17, 19, 20], "ftype": [9, 16], "san": [9, 16], "serif": [9, 16], "padding_x": [9, 16], "padding_i": [9, 16], "build_block": 9, "arrowfac": 9, "color": [9, 19, 20], "5px": 9, "min_fsiz": [9, 16], "15": [9, 11, 16, 19, 20], "attr": 9, "formatt": [9, 16], "get_cont": 9, "circlefac": [9, 16, 20], "et": [9, 10, 11, 14, 15, 16, 17, 18, 20], "piec": [9, 16, 20], "compute_fs": 9, "zx": [9, 16], "zy": [9, 16], "in_aligned_viewport": 9, "htmlface": 9, "imgfac": [9, 20], "img_path": [9, 20], "legendfac": 9, "colormap": [9, 16], "outlinefac": 9, "collapsing_height": 9, "piechartfac": 9, "compute_pi": 9, "rectfac": [9, 16], "scalefac": [9, 16], "scale_rang": [9, 16], "tick_width": [9, 16], "80": [9, 16], "line_width": [9, 16], "0f": [9, 16], "selectedcirclefac": 9, "selectedfac": 9, "selectedrectfac": 9, "seqfac": [9, 16, 20], "poswidth": [9, 16], "seqmotiffac": [9, 16, 20], "motif": [9, 16, 20], "build_region": 9, "region": 9, "stackedbarfac": 9, "whatev": 9, "textfac": [9, 16, 20], "alignedgrid": 9, "facecontain": 9, "grid": 9, "horizont": [9, 16], "idea": [9, 11, 18, 19], "header": [9, 11, 16], "footer": [9, 16], "col": [9, 20], "face1": 9, "face2": 9, "add_fac": [9, 11, 16, 20], "make_fac": 9, "karg": [9, 20], "attribut": [9, 10, 11, 14, 15, 16, 17, 20], "node_style_default": 9, "draw_descend": [9, 16], "mark": 9, "hz_line_width": [9, 16, 20], "pixel": [9, 11, 16, 20], "normal": [9, 15, 17, 18, 19, 20], "vt_line_width": [9, 16, 20], "vertic": [9, 16], "init": 9, "aligned_fac": [9, 16], "legend": 9, "set_node_styl": [9, 16], "set_tree_styl": [9, 16], "cased_nam": 9, "txt": 9, "active_fac": 9, "active_face_po": 9, "add_legend": [9, 16], "variabl": [9, 14, 16], "discret": [9, 16], "value_rang": [9, 16], "color_rang": [9, 16], "aligned_panel_foot": [9, 16], "aligned_panel_head": [9, 16], "get_legend": 9, "selected_fac": 9, "selected_face_po": 9, "layoutgenomiccontext": 9, "nside": 9, "conservation_threshold": 9, "70": [9, 16, 20], "gene_nam": 9, "tooltip_prop": 9, "anchor_stroke_color": 9, "anchor_stroke_width": 9, "3px": 9, "non_conserved_color": 9, "d0d0d0": 9, "collapse_conserv": 9, "collapse_by_conserv": 9, "get_context": 9, "get_tooltip": 9, "layoutbranchlength": 9, "branch_top": [9, 11, 16], "8d8d8d": 9, "layoutbranchsupport": 9, "branch_bottom": [9, 11, 16], "fa8072": 9, "layoutleafnam": 9, "branch_right": [9, 11, 16], "layoutnumberleav": 9, "collapsed_onli": [9, 11, 16], "layoutoutlin": 9, "lightgrai": 9, "layoutpfamdomain": 9, "pfam": 9, "layoutsmartdomain": 9, "smart": [9, 16], "21": 9, "layoutbestnam": 9, "best_nam": 9, "best": [9, 10, 15, 18, 20], "layoutbigg": 9, "bigg": 9, "layoutcard": 9, "card": 9, "layoutcazi": 9, "cazi": 9, "layoutevolev": 9, "speciation_color": 9, "blue": [9, 16, 20], "duplication_color": 9, "red": [9, 16, 20], "layoutkeggenzym": 9, "kegg_enzym": 9, "kegg": 9, "enzym": 9, "layoutkeggmodul": 9, "kegg_modul": 9, "11": [9, 15, 16, 19], "layoutkeggnumb": 9, "kegg_numb": 9, "layoutkeggpathwai": 9, "kegg_pathwai": 9, "pathwai": 9, "layoutlastcommonancestor": 9, "rect_width": 9, "1000": [9, 11, 16], "shown": [9, 15, 16, 20], "get_color": 9, "layoutpdb": 9, "pdb": 9, "layoutproteinnam": 9, "prot_nam": 9, "layoutscientificnam": 9, "layoutetediffdist": 9, "diff": 9, "diff_node_color": 9, "a50000": 9, "diff_node_s": 9, "layouthumanog": 9, "og": 9, "human_orth_prop": 9, "human_orth": 9, "6b92d6": 9, "layoutucsc": 9, "ucsc": 9, "nodecolor": 9, "800000": 9, "nodes": 9, "textcolor": 9, "c43b5d": 9, "layoutucsctran": 9, "tran": 9, "ucsc_trans_prop": 9, "ucsc_tran": 9, "get_layout_evoltyp": 9, "get_layout_gnam": 9, "get_layout_lca_rect": 9, "get_layout_ogs_egg5": 9, "get_layout_scinam": 9, "layoutalign": 9, "700": 9, "rang": [9, 15, 16, 20], "summarize_inner_nod": 9, "layoutautonam": 9, "auto": 9, "text_color": 9, "grei": 9, "layoutcuratednam": 9, "layouteukog": 9, "euk": 9, "layoutpreferrednam": 9, "fb3640": 9, "layoutscinam": 9, "layoutse": 9, "seed": [9, 11], "layoutbarplot": 9, "200": [9, 16, 20], "size_prop": 9, "color_prop": 9, "color_gradi": [9, 16], "taxdump_fil": 10, "transpar": [10, 16, 17, 20], "connector": 10, "connect": [10, 11, 17, 19], "system": [10, 20], "download": [10, 15, 17], "site": 10, "annotate_tre": 10, "deriv": [10, 20], "get_broken_branch": 10, "taxa_lineag": 10, "n2content": 10, "monophylet": [10, 11, 19], "well": [10, 15, 19], "affect": [10, 15, 19, 20], "experiment": 10, "get_common_nam": 10, "get_descendant_taxa": [10, 17], "intermediate_nod": [10, 17], "rank_limit": 10, "collapse_subspeci": [10, 17], "return_tre": [10, 17], "get_fuzzy_name_transl": 10, "sim": 10, "score": [10, 15, 19], "taxa": [10, 14], "similar": [10, 12, 16, 17, 19], "min": 10, "report": [10, 17], "get_lineag": [10, 17], "hierarch": [10, 11, 19, 20], "get_lineage_transl": 10, "get_name_transl": [10, 17], "get_rank": [10, 17], "get_taxid_transl": [10, 17], "try_synonym": 10, "get_topologi": [10, 17], "complet": [10, 15, 16, 19, 20], "kept": [10, 11, 16, 17, 19, 20], "rid": 10, "strain": 10, "upper": [10, 19], "translate_to_nam": [10, 17], "update_taxonomy_databas": [10, 17], "latest": [10, 17], "taxdump": [10, 17], "tar": [10, 17], "gz": [10, 17], "locat": [10, 19, 20], "tax": 10, "gtdb": [10, 14], "get_name_lineag": 10, "taxnam": 10, "anoth": [10, 11, 16, 19], "gtdbtaxdump": 10, "consist": [11, 16, 17, 19], "hampshir": [11, 19], "add_child": [11, 19], "supli": 11, "add_children": 11, "add_face_smartview": 11, "fix": [11, 15], "alwai": [11, 15, 18, 19], "attach": [11, 15, 16, 20], "independ": [11, 16, 19, 20], "go": [11, 18, 19], "posibl": 11, "add_face_treeview": 11, "integ": 11, "bottom": [11, 16, 20], "behind": 11, "add_featur": 11, "pr_name": 11, "pr_valu": 11, "add_prop": [11, 16, 17, 19, 20], "add_sist": [11, 19], "include_root": 11, "up": [11, 14, 18, 19, 20], "check_monophyli": [11, 19], "is_monophylet": 11, "clade_typ": 11, "leaves_extra": 11, "being": [11, 15, 19], "monophyli": [11, 14], "collapsed_fac": 11, "ref_tre": 11, "use_collater": 11, "min_support_sourc": 11, "min_support_ref": 11, "has_dupl": 11, "expand_polytomi": 11, "max_treeko_splits_to_be_artifact": 11, "ref_tree_attr": 11, "source_tree_attr": 11, "robinson": 11, "fould": 11, "symmetr": 11, "share": [11, 17, 19], "edg": [11, 16, 19], "cophenetic_matrix": 11, "cophenet": 11, "matrix": 11, "z": 11, "gist": 11, "github": [11, 16, 17], "279f9009f46bf675e3a890c19191158b": 11, "orderless": 11, "Then": 11, "xor": 11, "both": [11, 15, 16, 19, 20], "those": [11, 15, 16], "One": [11, 16, 18, 19, 20], "optim": 11, "sinc": [11, 15, 17, 18, 19], "itself": [11, 19], "zero": [11, 19], "itertool": 11, "combin": [11, 14, 15, 17], "rather": [11, 15, 17], "permut": [11, 18], "our": [11, 15, 16, 18, 19, 20], "theta": 11, "2n": 11, "o": [11, 16, 19, 20], "great": 11, "realiti": 11, "speed": [11, 15], "thing": [11, 18], "dimension": 11, "cpickl": [11, 19], "protocol": 11, "serialis": [11, 19], "thu": [11, 15, 16, 19, 20], "exclud": [11, 19], "As": [11, 15, 16, 19], "whole": [11, 15, 17, 19, 20], "clone": [11, 19], "slower": [11, 19], "recommend": [11, 19], "deepcopi": [11, 19], "slowest": [11, 19], "complex": [11, 16, 18, 19], "even": [11, 15, 16, 17, 19, 20], "etc": [11, 16, 18, 20], "del_featur": 11, "perman": 11, "del_prop": [11, 19], "prop_nam": [11, 19], "prevent_nondicotom": 11, "preserve_branch_length": [11, 19], "transfer": [11, 19], "until": 11, "occur": 11, "among": [11, 15, 16, 19], "to_str": [11, 15, 17, 18, 19], "levelord": [11, 12, 19], "detach": 11, "conserv": 11, "mechan": 11, "past": [11, 19], "pair": [11, 15, 16, 20], "lai": 11, "pass": [11, 15, 16, 17, 18, 19, 20], "won": 11, "recomput": 11, "map_prop": 11, "polytomy_size_limit": 11, "skip_large_polytomi": 11, "solut": [11, 19], "multifurc": [11, 14], "pleas": 11, "binari": 11, "exponenti": 11, "feasibl": 11, "105": [11, 16, 20], "945": 11, "10395": 11, "135135": 11, "2027025": 11, "ajmonlin": 11, "2010": 11, "darwin": 11, "php": 11, "show_branch_length": [11, 16, 20], "show_branch_support": [11, 16, 20], "launch": 11, "interact": [11, 14], "session": [11, 18, 20], "__name__": [11, 20], "adress": 11, "listen": [11, 16], "static": [11, 16, 20], "from_parent_child_t": 11, "parent_child_t": 11, "tabl": [11, 16, 20], "relationship": [11, 15, 19], "from_skbio": 11, "skbio_tre": 11, "map_attribut": 11, "scikit": 11, "bio": 11, "treenod": 11, "from_skibio": 11, "skbiotre": 11, "get_cached_cont": [11, 18, 19], "container_typ": 11, "leaves_onli": 11, "serv": [11, 17], "cach": [11, 14, 18], "And": [11, 15, 19, 20], "themselv": [11, 19], "get_children": 11, "get_closest_leaf": 11, "closest": 11, "get_dist": [11, 19], "target": [11, 16, 19], "target2": 11, "get_farthest_leaf": [11, 19], "get_farthest_nod": [11, 19], "get_midpoint_outgroup": [11, 19], "divid": 11, "get_monophylet": [11, 19], "consid": [11, 15, 19], "exclus": [11, 19], "get_sist": 11, "get_topology_id": 11, "bunch": 11, "without": [11, 15, 19], "sure": 11, "befor": [11, 16, 18, 19, 20], "hop": 11, "img_styl": [11, 20], "_get_styl": 11, "init_from_et": 11, "init_from_newick": 11, "is_collaps": 11, "_get_collaps": 11, "is_initi": 11, "_get_initi": 11, "is_root": [11, 16, 18, 19], "iter_prepostord": 11, "postord": [11, 19], "flag": [11, 15, 19], "visit": [11, 19], "leaf_nam": [11, 20], "pop_child": 11, "child_idx": 11, "uniformli": 11, "42": 11, "retain": 11, "minimum": 11, "k": [11, 18, 19], "remove_child": [11, 19], "exit": 11, "longer": [11, 20], "remove_children": 11, "remove_sist": 11, "file_nam": 11, "px": [11, 20], "dpi": [11, 20], "90": [11, 16, 20], "imag": [11, 14, 16], "svg": [11, 16, 20], "pdf": [11, 16, 20], "png": [11, 20], "mm": [11, 15, 20], "millimet": [11, 20], "inch": [11, 20], "resolut": [11, 20], "per": [11, 15, 20], "reverse_children": 11, "robinson_fould": [11, 19], "prop_t1": 11, "prop_t2": 11, "unrooted_tre": [11, 19], "correct_by_polytomy_s": 11, "min_support_t1": 11, "min_support_t2": 11, "rf": [11, 19], "rf_max": [11, 19], "edges_t1": 11, "edges_t2": 11, "discarded_edges_t1": 11, "discarded_edges_t2": 11, "expand": [11, 19], "absolut": [11, 15], "search_ancestor": [11, 19], "condit": [11, 12, 16, 18, 19], "search_descend": [11, 19], "search_leaves_by_nam": [11, 19], "search_nod": [11, 15, 19], "set_styl": [11, 16, 20], "node_styl": [11, 20], "doubl": 11, "_get_sm_styl": 11, "sort_descend": 11, "delete_orphan": 11, "swap_children": 11, "show_intern": [11, 15, 19], "compact": [11, 18, 19], "py": [11, 16, 20], "px0": 11, "cascad": 11, "ascii": 11, "exactli": 11, "overrid": 11, "three": [11, 15, 16, 18, 19], "bf": 11, "depth": [11, 19], "df": 11, "preorder": [11, 19], "someth": [12, 18], "re": [12, 18, 19, 20], "satisfi": [12, 16], "constraint": 12, "strongli": [12, 19], "restrict": 12, "keyword": 12, "constructor": [12, 19, 20], "context": [12, 16, 18], "understand": [14, 16], "faster": [14, 15], "lookup": 14, "concaten": 14, "solv": 14, "overview": 14, "taxonom": [14, 17], "date": 14, "aspect": 14, "less": [14, 19], "outsid": 14, "suit": [14, 16], "most": [15, 16, 17, 18, 19], "molecular": [15, 16, 20], "homolog": 15, "deal": [15, 19], "while": [15, 17, 20], "ancestr": 15, "direct": 15, "consequ": 15, "msa": [15, 16], "document": [15, 16, 20], "applic": 15, "unalign": 15, "mai": [15, 19], "fasta_txt": 15, "seqa": 15, "maeipdetiqqfmalt": 15, "hniavqylsefgtddikdrreeah": 15, "seqb": 15, "maeipdatiqqfmaltnvshniavqi": 15, "efgtddqkdrreeah": 15, "seqc": 15, "maeipdatiq": 15, "altnvshniavqylsefgtddqpdrreeah": 15, "seqd": 15, "maeapdetiqqfmaltnvshniavqylsefg": 15, "reeah": 15, "time": [15, 17, 18, 19, 20], "strict": [15, 19], "perfect": 15, "onc": [15, 16, 17, 19, 20], "through": [15, 16, 17, 19, 20], "hniavqylsefgdlnealnsyyasqtddikdrreeah": 15, "efgdlnealnsyyayqtddqkdrreeah": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeah": 15, "maeapdetiqqfmaltnvshniavqylsefgdln": 15, "iphylip_txt": 15, "76": 15, "maeipdetiq": 15, "qfmalt": 15, "niavqylsef": 15, "gdlnealnsi": 15, "yasqtddikd": 15, "rreeahqfma": 15, "qfmaltnvsh": 15, "niavqi": 15, "ef": [15, 19], "yayqtddqkd": 15, "altnvsh": 15, "yasqtddqpd": 15, "maeapdetiq": 15, "gdlneal": 15, "reeahq": 15, "ltnvshqfma": 15, "ltnvsh": 15, "fma": 15, "usual": [15, 17, 19], "now": [15, 16, 18, 19, 20], "let": [15, 16, 18, 19, 20], "fmaltnvsh": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqfmaltnvshqfmaltnvsh": 15, "efgdlnealnsyyayqtddqkdrreeahqfmaltnvsh": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqf": 15, "maltnvshqfmaltnvsh": 15, "efgdlnealnsi": 15, "yayqtddqkdrreeahqfmaltnvsh": 15, "altnvshnia": 15, "vqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "maeapd": 15, "etiqqfmaltnvshniavqylsefgdln": 15, "reload": 15, "sametre": 15, "recov": 15, "benefit": 15, "programm": [15, 16, 20], "built": [15, 16, 19, 20], "conveni": [15, 17, 19], "alg": 15, "dme_001": 15, "hniavqylsefgdln": 15, "yyasqtddikdrreeah": 15, "dme_002": 15, "cfa_001": 15, "mms_001": 15, "hsa_001": 15, "ptr_002": 15, "fmaltnvshniavqi": 15, "yqtddqkdrreeah": 15, "mmu_002": 15, "hsa_002": 15, "maeapdetiqqfm": 15, "ltnvshniavqylsefgdln": 15, "mmu_001": 15, "ptr_001": 15, "gene_tree_nw": 15, "species_tree_nw": 15, "hsa": [15, 20], "ptr": [15, 20], "mmu": 15, "cfa": [15, 20], "dme": [15, 20], "genetre": 15, "sptree": 15, "recon_tre": 15, "separ": [15, 19], "obtain": [15, 19], "often": [15, 18, 19], "establish": [15, 19], "behavior": 15, "get_species_nam": 15, "node_name_str": 15, "underscor": 15, "spcode": [15, 17], "code2nam": [15, 20], "drosophila": [15, 20], "melanogast": [15, 20], "homo": [15, 16, 17, 20], "sapien": [15, 17, 20], "troglodyt": [15, 17, 20], "mu": [15, 17, 20], "musculu": [15, 17, 20], "cani": [15, 20], "familiari": [15, 20], "disabl": [15, 19], "overwriten": 15, "mynewick": 15, "chimp": [15, 20], "dog": [15, 20], "mous": [15, 16, 20], "fly": [15, 16, 20], "charleston": 15, "1997": 15, "paralogi": 15, "houben": 15, "2009": 15, "appli": [15, 16, 17, 19, 20], "threshold": [15, 16], "rise": 15, "adjust": [15, 16, 20], "human_seq": 15, "ev": 15, "join": 15, "interest": [15, 19], "filter": [15, 19], "fseq": 15, "slist": 15, "startswith": [15, 16, 20], "besid": 15, "predict": 15, "labl": 15, "predefin": [15, 20], "explain": 15, "strictli": [15, 19], "taxonomic_info": 15, "fir": 15, "inparalog": 15, "ortholog": 15, "elif": [15, 16, 20], "outparalog": 15, "notic": 15, "state": 15, "addition": [15, 19], "phylo": 15, "paralog": 15, "similarli": [15, 19], "therefor": [15, 16, 19], "certain": [15, 19], "although": [15, 16, 19, 20], "precis": 15, "approach": [15, 17, 19], "synonym": 15, "rate": 15, "proxi": 15, "diverg": 15, "al": 15, "kalinka": 15, "2001": 15, "aim": 15, "gradient": 15, "primat": [15, 17, 19, 20], "mammal": [15, 20], "vertebr": 15, "abov": [15, 16, 17, 19, 20], "categori": 15, "orangutan": 15, "fish": [15, 20], "relative_dist": 15, "non": 15, "rat": 15, "purpos": 15, "humana": 15, "chimpa": 15, "dup1": 15, "humanb": 15, "chimpb": 15, "mousea": 15, "dup3": 15, "humanc": 15, "chimpc": 15, "dup2": 15, "humand": 15, "ratc": 15, "mousec": 15, "distant": [15, 19], "lett": 15, "hsa_003": 15, "hsa_004": 15, "ptr_004": 15, "mmu_004": 15, "older": 15, "belong": [15, 20], "hominid": 15, "macaca": 15, "mulata": 15, "metazoa": [15, 17, 19], "correspondig": 15, "age2nam": 15, "event1": 15, "event2": 15, "lead": 15, "vari": 15, "assist": [15, 19], "autodetect": 15, "miss": [15, 19], "useless": 15, "observ": 15, "subpart": [15, 19], "becaus": [15, 16], "combinatori": 15, "background": 15, "enorm": 15, "few": [15, 18], "hundr": 15, "ten": 15, "thousand": 15, "here": [15, 16, 17, 19, 20], "human_1": 15, "chimp_1": 15, "human_2": 15, "chimp_2": 15, "chimp_3": 15, "fish_1": 15, "human_3": 15, "fish_3": 15, "yeast_2": 15, "yeast_1": 15, "yeast": [15, 19], "ignor": [15, 17], "ntree": 15, "ndup": 15, "spt": 15, "map_featur": 15, "effici": [15, 17, 18], "significantli": 15, "much": 15, "simpler": 15, "previou": [15, 16, 18, 19], "easili": [15, 17, 19, 20], "novel": 16, "enhanc": 16, "introduc": [16, 17], "v4": [16, 17], "essenti": [16, 17, 19], "foundat": 16, "v3": 16, "fundament": 16, "compon": 16, "highli": [16, 20], "adapt": [16, 17], "backbon": 16, "variou": 16, "choos": [16, 20], "treelayout": 16, "graph": [16, 19, 20], "geometr": [16, 20], "shape": [16, 20], "sequencefac": [16, 20], "These": [16, 17, 19], "upgrad": 16, "entir": [16, 19], "individu": 16, "act": [16, 20], "hook": [16, 20], "framework": 16, "drawn": [16, 20], "drawer": 16, "henc": 16, "understood": [16, 19, 20], "rule": [16, 20], "scheme": [16, 19], "fulli": [16, 17, 20], "integr": [16, 17, 20], "interfac": [16, 20], "gui": [16, 19, 20], "simpli": [16, 20], "advantag": [16, 20], "interrupt": [16, 20], "continu": [16, 20], "execut": [16, 20], "made": [16, 20], "quit": [16, 18, 20], "special": [16, 18, 19, 20], "dure": [16, 20], "util": [16, 17], "environ": 16, "ipython": 16, "jupyt": 16, "notebook": 16, "below": [16, 19, 20], "demonstr": 16, "usag": 16, "explore_standalon": 16, "sep": 16, "16": [16, 20], "2021": 16, "13": [16, 19], "09": [16, 19], "58": 16, "copyright": 16, "credit": 16, "licens": 16, "29": 16, "help": [16, 17], "action": [16, 19], "bottl": 16, "v0": 16, "25": [16, 20], "wsgirefserv": 16, "hit": 16, "ctrl": 16, "127": 16, "02": 16, "nov": 16, "2023": 16, "19": 16, "303": 16, "106": 16, "30": [16, 20], "nodecount": 16, "all_select": 16, "all_act": 16, "555": 16, "284": 16, "40000000000003": 16, "za": 16, "33333333333333337": 16, "16666666666666666": 16, "3333333333333335": 16, "333333333333333": 16, "5b": 16, "5d": 16, "22default": 16, "3abranch": 16, "22": 16, "2c": 16, "3aleaf": 16, "1765": 16, "explore_show": 16, "click": 16, "decid": [16, 19], "Or": [16, 17, 19, 20], "trig": 16, "targer": 16, "major": 16, "smaller": [16, 19], "whether": 16, "deactiv": 16, "minimap": 16, "hover": 16, "cursor": 16, "tend": 16, "occupi": 16, "area": [16, 20], "button": 16, "input": [16, 17, 19], "histori": 16, "modtifi": 16, "insensit": 16, "lower": [16, 19], "sensit": 16, "prefix": 16, "regexp": 16, "power": [16, 18], "straightforward": 16, "ch": [16, 18], "regex": [16, 18], "citrobact": 16, "werkmanii": 16, "younga": 16, "uba": 16, "spx": 16, "uba2009": 16, "rokubacterial": 16, "sp": [16, 17], "least": [16, 18], "digit": 16, "escherichia": 16, "sp002965065": 16, "sp005281345": 16, "equal": [16, 19, 20], "edit": 16, "trigger": 16, "editor": 16, "four": [16, 20], "regard": [16, 19, 20], "pure": 16, "obligatori": 16, "tree_layout": 16, "mytreelayout": 16, "append": [16, 19], "frame": 16, "treelayout_1": 16, "futher": 16, "modify_tree_styl": 16, "treestyle_1": 16, "mylegend": 16, "green": [16, 19, 20], "treestyle_legend": 16, "attributt": 16, "foreground": [16, 20], "thats": 16, "ff0000": [16, 20], "hex": 16, "0030c1": 16, "outline_line_color": 16, "border": [16, 20], "000000": [16, 20], "outline_line_width": 16, "outline_color": 16, "e5e5e5": 16, "outline_opac": 16, "vt_line_color": [16, 20], "verticl": 16, "hz_line_color": [16, 20], "hz_line_typ": [16, 20], "vt_line_typ": [16, 20], "pf": 16, "piexl": 16, "fo": 16, "triangle_node_styl": 16, "brown": [16, 20], "964b00": 16, "modify_node_styl": 16, "corner": 16, "nodestyle_triangl": 16, "must": [16, 19, 20], "leaf_styl": 16, "root_styl": 16, "nodestyle_differ": 16, "extern": [16, 19, 20], "outlinedfac": 16, "dengzq1234": 16, "ete4_galleri": 16, "around": [16, 20], "modify_face_posit": 16, "hola": [16, 20], "mundo": [16, 20], "faceposition_bottom": 16, "pile": [16, 20], "faceposition_align": 16, "recycl": [16, 20], "notabl": 16, "directli": [16, 19, 20], "faceposition_collaps": 16, "faceposition_al": 16, "config": [16, 20], "permit": [16, 20], "veri": [16, 19, 20], "top_textfac": 16, "courier": 16, "togeth": [16, 19], "bottom_textfac": 16, "modify_face_properti": 16, "faceproperties_textfac": 16, "sent": [16, 20], "wrap": 16, "modfii": 16, "insid": [16, 18], "vowel_node_layout": 16, "vowel": [16, 19, 20], "advance_layout": 16, "vowel_tree_styl": 16, "conost": 16, "combinedlayout_bas": 16, "vowel_color": 16, "conostant_color": 16, "vowel_node_s": 16, "conostant_node_s": 16, "ensur": [16, 20], "goe": 16, "addit": [16, 17, 18, 19], "super": [16, 20], "vowel_textfac": 16, "conostant_textfac": 16, "combinedlayout_object": 16, "a3": [16, 20], "b3": [16, 20], "b4": [16, 20], "c1": [16, 20], "c2": [16, 20], "c3": [16, 20], "nst1": [16, 20], "lightsteelblu": [16, 20], "nst2": [16, 20], "moccasin": [16, 20], "nst3": [16, 20], "darkseagreen": [16, 20], "nst4": [16, 20], "khaki": [16, 20], "n3": [16, 20], "n4": [16, 20], "ancestor_a": 16, "ancestor_b": 16, "ancestor_c": 16, "ancestor_d": 16, "get_tree_styl": 16, "get_background": 16, "bigger": 16, "node_background": [16, 20], "d1": 16, "d2": 16, "get_node_fac": 16, "lca_fac": 16, "white": [16, 20], "rotate_text": 16, "colorstrip": 16, "numer": [16, 17], "count": [16, 19], "randint": [16, 20], "layout_tree_styl": 16, "sample1": 16, "150": [16, 20], "layout_barplot": 16, "rect_fac": 16, "skyblu": 16, "barplot_layout": 16, "barplot": 16, "matplotlib": 16, "mpl": 16, "np": 16, "frequenc": 16, "darkr": [16, 20], "layout_heatmap": 16, "mincolor": 16, "maxcolor": 16, "maxval": 16, "max": [16, 20], "minval": 16, "mix": 16, "fade": 16, "linear": 16, "interpol": 16, "to_rgb": 16, "to_hex": 16, "get_heatmapfac": 16, "ratio": [16, 20], "gradient_color": 16, "print_frequnc": 16, "treefil": 16, "aln": 16, "faa": 16, "fastafil": 16, "phy003i7zj_chick": 16, "tmsqfnfssapagggfsfstpkt": 16, "name2seq": 16, "head": 16, "lstrip": 16, "rstrip": 16, "layout_alnface_grai": 16, "seq_fac": 16, "800": 16, "layout_alnface_compact": 16, "compactseq": [16, 20], "layout_seqfac": 16, "compact_aln": 16, "gray_aln": 16, "msa_layout": 16, "aqak": [16, 20], "ikgskkaikvfssa": [16, 20], "aperlqeygsiftda": [16, 20], "glqrrprhriqsk": [16, 20], "alqeklkdfpvcvstkpepeddaeeglgglpsn": [16, 20], "issvsslllfnttenlykkyvfldplag": [16, 20], "thvmlgaeteeklfdaplsiskreqleqqvpenyfyvpd": [16, 20], "lgqvpeidvpsylpdlpgiandlmyiadlgpgiapsapgtipelptfhtevaeplkvgelgsgmgagpgtp": [16, 20], "ahtpssldtphfvfqtykmgapplppstaapvgqgarqddssssaspsvqgaprevvdpsggwatllesir": [16, 20], "qaggigkaklrsmkerklekqqqkeqeqvratsqgghl": [16, 20], "msdlfnklvmrrkgisgkgpgagdgpggafa": [16, 20], "rvsdsipplpppqqpqaed": [16, 20], "mixed_motif": [16, 20], "rgradient": [16, 20], "arial": [16, 20], "long": [16, 19, 20], "clip": [16, 20], "101": [16, 20], "pink": [16, 20], "155": [16, 20], "180": 16, "purpl": [16, 19, 20], "160": [16, 20], "190": [16, 20], "24": 16, "yellow": [16, 19, 20], "191": [16, 20], "orang": [16, 20], "201": [16, 20], "250": [16, 20], "351": [16, 20], "370": [16, 20], "gold": [16, 20], "420": [16, 20], "simple_motif": [16, 20], "120": [16, 20], "300": [16, 20], "hello": [16, 18, 20], "box_motif": [16, 20], "ref": [16, 20], "85": [16, 20], "110": [16, 20], "125": [16, 20], "layout_domain": 16, "blank": [16, 20], "domain_layout": 16, "ncbi_taxonomi": 17, "gtdb_taxonomi": 17, "offer": 17, "vice": 17, "versa": 17, "fetch": 17, "comprehens": [17, 19], "organ": 17, "daili": 17, "portal": 17, "ftp": 17, "releas": 17, "dmp": 17, "taxon": 17, "taxonomyi": 17, "commonli": [17, 19], "signifi": 17, "entiti": 17, "genet": 17, "9606": 17, "On": 17, "hand": 17, "distribut": 17, "sqlite": 17, "fullfil": 17, "convers": [17, 20], "third": [17, 19], "parti": 17, "nick": 17, "youngblut": 17, "gtdb_to_taxdump": 17, "emploi": 17, "alreadi": [17, 18, 19, 20], "preprar": 17, "attempt": 17, "600mb": 17, "72mb": 17, "skip": 17, "answer": 17, "internet": 17, "fname": 17, "gtdb202dump": 17, "taxid2nam": 17, "9443": 17, "name2taxid": 17, "bacteria": 17, "629395": 17, "further": 17, "131567": 17, "2759": 17, "33154": 17, "33208": 17, "6072": 17, "33213": 17, "33511": 17, "7711": 17, "89593": 17, "7742": 17, "7776": 17, "117570": 17, "117571": 17, "8287": 17, "1338369": 17, "32523": 17, "32524": 17, "40674": 17, "32525": 17, "9347": 17, "1437010": 17, "314146": 17, "376913": 17, "314293": 17, "9526": 17, "314295": 17, "9604": 17, "207598": 17, "9605": 17, "cellular": 17, "eukaryota": 17, "opisthokonta": 17, "eumetazoa": 17, "bilateria": 17, "deuterostomia": 17, "chordata": 17, "craniata": 17, "vertebrata": 17, "gnathostomata": 17, "teleostomi": 17, "euteleostomi": 17, "sarcopterygii": 17, "dipnotetrapodomorpha": 17, "tetrapoda": 17, "amniota": 17, "mammalia": 17, "theria": 17, "eutheria": 17, "boreoeutheria": 17, "euarchontoglir": 17, "haplorrhini": 17, "simiiform": 17, "catarrhini": 17, "hominoidea": 17, "hominida": [17, 20], "hominina": 17, "doesn": [17, 18], "ve": 17, "facilit": [17, 19], "offici": 17, "recogn": 17, "easier": 17, "neanderthalensi": 17, "subsp": 17, "denisova": 17, "heidelbergensi": 17, "environment": 17, "sampl": 17, "subspeci": [17, 20], "2665952": 17, "2665953": 17, "1425170": 17, "unclassifi": 17, "2813598": 17, "2813599": 17, "f__thorarchaeacea": 17, "gb_gca_003662765": 17, "gb_gca_003662805": 17, "gb_gca_013138615": 17, "s__mp8t": 17, "sp002825535": 17, "sp003345545": 17, "s__tekir": 17, "sp004524435": 17, "g__mp8t": 17, "genu": [17, 20], "sp002825465": 17, "sp004524565": 17, "sp004524595": 17, "s__smtz1": 17, "83": 17, "sp011364985": 17, "g__smtz1": 17, "sp011365025": 17, "sp001563325": 17, "g__tekir": 17, "14": [17, 20], "sp004524445": 17, "g__shmx01": 17, "s__shmx01": 17, "sp008080745": 17, "s__owc5": 17, "sp003345595": 17, "g__owc5": 17, "f__tho": 17, "sp003345555": 17, "g__jacael01": 17, "s__jacael01": 17, "sp013388835": 17, "g__b65": 17, "g9": 17, "s__b65": 17, "sp003662765": 17, "sp001563335": 17, "sp011364905": 17, "sp001940705": 17, "sp004376265": 17, "sp002825515": 17, "g__wtck01": 17, "s__wtck01": 17, "sp013138615": 17, "smallest": 17, "9598": 17, "10090": 17, "7707": 17, "8782": 17, "dendrochirotida": 17, "subfamili": 17, "superord": 17, "av": 17, "p__huberarchaeota": 17, "o__peptococcal": 17, "f__korarchaeacea": 17, "phylum": 17, "d__archaea": 17, "superkingdom": 17, "p__thermoproteota": 17, "c__korarchaeia": 17, "o__korarchaeal": 17, "d__bacteria": 17, "p__firmicutes_b": 17, "c__peptococcia": 17, "sibl": 17, "rememb": 17, "bacteriovorax": 17, "stolpii": 17, "bdellovibrionota": 17, "3018035": 17, "bdellovibrio": 17, "bacteriovoru": 17, "ancylobact": 17, "aquaticu": 17, "prota": 17, "protb": 17, "namespac": 17, "gb_gca_020833055": 17, "gb_gca_003344655": 17, "rs_gcf_000019605": 17, "rs_gcf_003948265": 17, "s__korarchaeum": 17, "sp020833055": 17, "g__korarchaeum": 17, "sp003344655": 17, "cryptofilum": 17, "protc": 17, "protd": 17, "annotate_dict": 17, "gtdb_spcode": 17, "realat": 18, "impos": 18, "regular": 18, "imagin": 18, "treematch": 18, "tp": 18, "okai": 18, "ones": 18, "But": [18, 19], "seem": 18, "Will": [18, 19], "len": [18, 19, 20], "tripl": 18, "freeli": [18, 19], "distinguish": 18, "parenthesi": 18, "compil": 18, "feel": 18, "variant": 18, "incorrect": 18, "exist": [18, 19], "sup": 18, "getattr": 18, "legibl": 18, "nchildren": 18, "did": [18, 19], "know": 18, "tell": 18, "Of": [18, 19], "cours": [18, 19], "neg": 18, "beforehand": 18, "n2leav": 18, "final": [18, 19, 20], "consol": 18, "comfort": 18, "sparingli": 18, "enjoi": 18, "bye": 18, "construct": [18, 19], "expected_result": 18, "xx": 18, "nsearch": 18, "win": 18, "emul": 19, "design": [19, 20], "formal": 19, "acycl": 19, "down": 19, "superior": 19, "longest": 19, "downward": 19, "topmost": 19, "Being": 19, "begin": 19, "reach": 19, "bottommost": 19, "inner": 19, "portion": 19, "view": [19, 20], "compris": 19, "proper": 19, "analogi": 19, "term": 19, "subset": 19, "entail": 19, "consider": 19, "remain": 19, "constant": 19, "nest": 19, "parenthes": 19, "nevertheless": 19, "uncommon": 19, "variat": 19, "control": [19, 20], "definit": 19, "cool": 19, "high": 19, "With": [19, 20], "familiar": 19, "genes_tre": 19, "export": [19, 20], "notat": 19, "new_tre": 19, "success": 19, "practic": 19, "distinct": 19, "concept": 19, "review": 19, "moreov": 19, "latter": 19, "reliabl": 19, "bootstrap": 19, "syntax": 19, "conceptu": 19, "That": 19, "master": [19, 20], "rooted_tre": 19, "navig": 19, "explanatori": 19, "q": 19, "m": 19, "boolean": 19, "becom": 19, "cd": 19, "node2label": 19, "collapsed_leaf": 19, "sai": 19, "deepest": 19, "larger": 19, "abcd": 19, "efg": 19, "processable_nod": 19, "sometim": [19, 20], "along": 19, "node3": 19, "cannot": 19, "statement": 19, "search_by_s": 19, "40": 19, "handi": 19, "matches2": 19, "para": 19, "poli": 19, "phylet": 19, "inde": 19, "paraphylet": 19, "nor": 19, "polyphylet": 19, "signific": 19, "slowdown": 19, "instantan": 19, "node2leav": 19, "later": [19, 20], "ancestor_jfc": 19, "confid": 19, "nodetyp": 19, "loop": 19, "overwrit": 19, "is_vowel": 19, "aeiou": 19, "higher": 19, "long_branch_nod": 19, "precomput": 19, "conf": 19, "enclos": 19, "bracket": 19, "plain": 19, "www": 19, "phylosoft": 19, "adh2": 19, "adh1": 19, "05": 19, "adhi": 19, "nematod": 19, "adhx": 19, "insect": [19, 20], "adh4": 19, "adh3": 19, "fungi": 19, "tag": 19, "averag": 19, "max_rf": 19, "norm_rf": 19, "effective_tree_s": 19, "ref_edges_in_sourc": 19, "source_edges_in_ref": 19, "source_subtre": 19, "common_edg": 19, "source_edg": 19, "ref_edg": 19, "treeko_dist": 19, "metric": 19, "examin": 19, "discard": 19, "mention": 19, "parts_t1": 19, "parts_t2": 19, "total": 19, "tree2": 19, "were": 19, "tree1": 19, "hold": 19, "partial": 19, "Such": 19, "orphan": 19, "never": 19, "unless": 19, "ok": 19, "r1": 19, "r6": 19, "names_librari": 19, "r2": 19, "r3": 19, "r4": 19, "r5": 19, "disconnect": 19, "contrast": 19, "removed_nod": 19, "unnecessari": 19, "fact": 19, "serious": 19, "care": 19, "mistak": 19, "intric": 19, "serial": 19, "internal_1": 19, "internal_2": 19, "lose": 19, "_0_": 19, "1_": 19, "_2_": 19, "3_": 19, "arbitrarili": 19, "bifurc": 19, "realli": 19, "softwar": 19, "intact": 19, "recurs": 19, "polynod": 19, "techniqu": 19, "polar": 19, "basal": 19, "crucial": 19, "prior": 19, "determin": [19, 20], "differenti": 19, "moment": [19, 20], "obvious": 19, "brother": 19, "opposit": 19, "toplog": 19, "incorpor": 19, "occurr": 19, "instal": 20, "scratch": 20, "invok": 20, "raster": 20, "pictur": 20, "break": 20, "a4": 20, "183": 20, "circular_styl": 20, "se": 20, "increas": 20, "branch_vertical_margin": 20, "adjac": 20, "semi": 20, "circumfer": 20, "arc_start": 20, "clock": 20, "arc_span": 20, "sphere": 20, "nstyle": 20, "cccccc": 20, "replic": 20, "heatmap": 20, "profilefac": 20, "face_grid_tutori": 20, "apart": 20, "margin": 20, "margin_top": 20, "margin_right": 20, "margin_left": 20, "margin_bottom": 20, "inner_bord": 20, "lightgreen": 20, "abc_layout": 20, "probabl": 20, "get_example_tre": 20, "bold": 20, "0f0f0f": 20, "style1": 20, "style2": 20, "0000aa": 20, "__main__": 20, "400": 20, "root_opening_factor": 20, "dre": 20, "008339": 20, "300613": 20, "596401": 20, "640858": 20, "753230": 20, "182035": 20, "106234": 20, "271621": 20, "046042": 20, "953250": 20, "061813": 20, "110769": 20, "204419": 20, "973467": 20, "humanfac": 20, "mousefac": 20, "dogfac": 20, "chimpfac": 20, "fishfac": 20, "flyfac": 20, "readi": 20, "namefac": 20, "009000": 20, "danio": 20, "rerio": 20, "code2desc": 20, "zebrafish": 20, "known": 20, "tropic": 20, "freshwat": 20, "minnow": 20, "cyprinida": 20, "fli": 20, "diptera": 20, "possess": 20, "wing": 20, "mesothorax": 20, "halter": 20, "hind": 20, "metathorax": 20, "member": 20, "biped": 20, "chimpanze": 20, "colloqui": 20, "extant": 20, "ap": 20, "rodent": 20, "lupu": 20, "domest": 20, "wolf": 20, "canida": 20, "ordercarnivora": 20, "mylayout": 20, "longnamefac": 20, "multilin": 20, "descfac": 20, "enumer": 20, "aa0000": 20, "9db0cf": 20, "img_fac": 20, "600": 20, "weight": 20, "proport": 20, "royalblu": 20, "manual": 20, "bubble_map": 20, "treefac": 20, "small_t": 20, "laef": 20, "tree_fac": 20, "tree_width": 20, "seq_motif_fac": 20, "plai": 20, "colorsi": 20, "pyqt6": 20, "qtcore": 20, "qtgui": 20, "qcolor": 20, "qpen": 20, "qbrush": 20, "qtwidget": 20, "qgraphicsrectitem": 20, "qgraphicssimpletextitem": 20, "qgraphicsellipseitem": 20, "interactiveitem": 20, "setcursor": 20, "pointinghandcursor": 20, "setacceptshoverev": 20, "hoverenterev": 20, "hide": 20, "dynamicitemfac": 20, "setparentitem": 20, "zvalu": 20, "setzvalu": 20, "setbrush": 20, "settext": 20, "setrect": 20, "boundingrect": 20, "setvis": 20, "hoverleaveev": 20, "random_color": 20, "hue": 20, "rgb": 20, "luminos": 20, "satur": 20, "hls_to_rgb": 20, "02x": 20, "255": 20, "ugly_name_fac": 20, "qgraphicsitem": 20, "masteritem": 20, "doc": 20, "No": 20, "setpen": 20, "nopen": 20, "ellips": 20, "tw": 20, "th": 20, "setpo": 20, "master_li": 20, "itemfac": 20, "forward": 20}, "objects": {"ete4": [[10, 0, 1, "", "GTDBTaxa"], [10, 0, 1, "", "NCBITaxa"], [7, 0, 1, "", "PhyloTree"], [11, 0, 1, "", "Tree"]], "ete4.GTDBTaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_lineage"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.NCBITaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_fuzzy_name_translation"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.PhyloTree": [[7, 1, 1, "", "__init__"], [7, 1, 1, "", "annotate_gtdb_taxa"], [7, 1, 1, "", "annotate_ncbi_taxa"], [7, 1, 1, "", "collapse_lineage_specific_expansions"], [7, 1, 1, "", "get_age"], [7, 1, 1, "", "get_age_balanced_outgroup"], [7, 1, 1, "", "get_descendant_evol_events"], [7, 1, 1, "", "get_farthest_oldest_leaf"], [7, 1, 1, "", "get_farthest_oldest_node"], [7, 1, 1, "", "get_my_evol_events"], [7, 1, 1, "", "get_speciation_trees"], [7, 1, 1, "", "get_species"], [7, 1, 1, "", "iter_species"], [7, 1, 1, "", "link_to_alignment"], [7, 1, 1, "", "ncbi_compare"], [7, 1, 1, "", "reconcile"], [7, 1, 1, "", "set_species_naming_function"], [7, 2, 1, "", "species"], [7, 1, 1, "", "split_by_dups"], [7, 1, 1, "", "write"]], "ete4.Tree": [[11, 1, 1, "", "__init__"], [11, 1, 1, "", "add_child"], [11, 1, 1, "", "add_children"], [11, 1, 1, "", "add_face"], [11, 1, 1, "", "add_face_smartview"], [11, 1, 1, "", "add_face_treeview"], [11, 1, 1, "", "add_feature"], [11, 1, 1, "", "add_features"], [11, 1, 1, "", "add_prop"], [11, 1, 1, "", "add_props"], [11, 1, 1, "", "add_sister"], [11, 1, 1, "", "ancestors"], [11, 1, 1, "", "check_monophyly"], [11, 3, 1, "", "children"], [11, 3, 1, "", "collapsed_faces"], [11, 1, 1, "", "common_ancestor"], [11, 1, 1, "", "compare"], [11, 1, 1, "", "cophenetic_matrix"], [11, 1, 1, "", "copy"], [11, 1, 1, "", "del_feature"], [11, 1, 1, "", "del_prop"], [11, 1, 1, "", "delete"], [11, 1, 1, "", "descendants"], [11, 1, 1, "", "describe"], [11, 1, 1, "", "detach"], [11, 3, 1, "", "dist"], [11, 1, 1, "", "edges"], [11, 1, 1, "", "expand_polytomies"], [11, 1, 1, "", "explore"], [11, 3, 1, "", "faces"], [11, 1, 1, "", "from_parent_child_table"], [11, 1, 1, "", "from_skbio"], [11, 1, 1, "", "get_cached_content"], [11, 1, 1, "", "get_children"], [11, 1, 1, "", "get_closest_leaf"], [11, 1, 1, "", "get_distance"], [11, 1, 1, "", "get_farthest_leaf"], [11, 1, 1, "", "get_farthest_node"], [11, 1, 1, "", "get_midpoint_outgroup"], [11, 1, 1, "", "get_monophyletic"], [11, 1, 1, "", "get_prop"], [11, 1, 1, "", "get_sisters"], [11, 1, 1, "", "get_topology_id"], [11, 3, 1, "", "id"], [11, 2, 1, "", "img_style"], [11, 1, 1, "", "init_from_ete"], [11, 1, 1, "", "init_from_newick"], [11, 2, 1, "", "is_collapsed"], [11, 2, 1, "", "is_initialized"], [11, 3, 1, "", "is_leaf"], [11, 1, 1, "", "is_monophyletic"], [11, 3, 1, "", "is_root"], [11, 1, 1, "", "iter_prepostorder"], [11, 1, 1, "", "ladderize"], [11, 1, 1, "", "leaf_names"], [11, 1, 1, "", "leaves"], [11, 3, 1, "", "level"], [11, 1, 1, "", "lineage"], [11, 3, 1, "", "name"], [11, 1, 1, "", "pop_child"], [11, 1, 1, "", "populate"], [11, 3, 1, "", "props"], [11, 1, 1, "", "prune"], [11, 1, 1, "", "remove_child"], [11, 1, 1, "", "remove_children"], [11, 1, 1, "", "remove_sister"], [11, 1, 1, "", "render"], [11, 1, 1, "", "resolve_polytomy"], [11, 1, 1, "", "reverse_children"], [11, 1, 1, "", "robinson_foulds"], [11, 3, 1, "", "root"], [11, 1, 1, "", "search_ancestors"], [11, 1, 1, "", "search_descendants"], [11, 1, 1, "", "search_leaves_by_name"], [11, 1, 1, "", "search_nodes"], [11, 1, 1, "", "set_outgroup"], [11, 1, 1, "", "set_style"], [11, 1, 1, "", "show"], [11, 3, 1, "", "size"], [11, 2, 1, "", "sm_style"], [11, 1, 1, "", "sort_descendants"], [11, 1, 1, "", "standardize"], [11, 3, 1, "", "support"], [11, 1, 1, "", "swap_children"], [11, 1, 1, "", "to_str"], [11, 1, 1, "", "to_ultrametric"], [11, 1, 1, "", "traverse"], [11, 1, 1, "", "unroot"], [11, 3, 1, "", "up"], [11, 1, 1, "", "write"]], "ete4.clustering": [[4, 4, 0, "-", "clustertree"]], "ete4.clustering.clustertree": [[4, 0, 1, "", "ClusterTree"]], "ete4.clustering.clustertree.ClusterTree": [[4, 1, 1, "", "__init__"], [4, 2, 1, "", "deviation"], [4, 1, 1, "", "get_dunn"], [4, 1, 1, "", "get_silhouette"], [4, 2, 1, "", "intercluster_dist"], [4, 2, 1, "", "intracluster_dist"], [4, 1, 1, "", "leaf_profiles"], [4, 1, 1, "", "link_to_arraytable"], [4, 2, 1, "", "profile"], [4, 1, 1, "", "set_distance_function"], [4, 2, 1, "", "silhouette"]], "ete4.core": [[5, 4, 0, "-", "operations"], [8, 4, 0, "-", "seqgroup"]], "ete4.core.operations": [[5, 0, 1, "", "Walker"], [5, 5, 1, "", "add_branch_values"], [5, 5, 1, "", "add_leaf_names"], [5, 5, 1, "", "assert_root_consistency"], [5, 5, 1, "", "common_ancestor"], [5, 5, 1, "", "create_dichotomic_sister"], [5, 5, 1, "", "farthest"], [5, 5, 1, "", "farthest_descendant"], [5, 5, 1, "", "insert_intermediate"], [5, 5, 1, "", "interchange_references"], [5, 5, 1, "", "join_branch"], [5, 5, 1, "", "ladderize"], [5, 5, 1, "", "make_name"], [5, 5, 1, "", "midpoint"], [5, 5, 1, "", "move"], [5, 5, 1, "", "populate"], [5, 5, 1, "", "populate_uniform"], [5, 5, 1, "", "populate_yule"], [5, 5, 1, "", "rehang"], [5, 5, 1, "", "remove"], [5, 5, 1, "", "resolve_polytomy"], [5, 5, 1, "", "root_at"], [5, 5, 1, "", "set_midpoint_outgroup"], [5, 5, 1, "", "set_outgroup"], [5, 5, 1, "", "sort"], [5, 5, 1, "", "swap_props"], [5, 5, 1, "", "to_dendrogram"], [5, 5, 1, "", "to_ultrametric"], [5, 5, 1, "", "traverse"], [5, 5, 1, "", "traverse_bfs"], [5, 5, 1, "", "unroot"], [5, 5, 1, "", "update_size"], [5, 5, 1, "", "update_sizes_all"], [5, 5, 1, "", "update_sizes_from"], [5, 5, 1, "", "walk"]], "ete4.core.operations.Walker": [[5, 1, 1, "", "add_next_branch"], [5, 2, 1, "", "first_visit"], [5, 1, 1, "", "go_back"], [5, 2, 1, "", "has_unvisited_branches"], [5, 2, 1, "", "node"], [5, 2, 1, "", "node_id"]], "ete4.core.seqgroup": [[8, 0, 1, "", "SeqGroup"]], "ete4.core.seqgroup.SeqGroup": [[8, 1, 1, "", "__init__"], [8, 1, 1, "", "get_entries"], [8, 1, 1, "", "get_seq"], [8, 1, 1, "", "iter_entries"], [8, 1, 1, "", "set_seq"], [8, 1, 1, "", "write"]], "ete4.parser": [[6, 4, 0, "-", "newick"], [6, 4, 0, "-", "nexus"]], "ete4.parser.newick": [[6, 6, 1, "", "NewickError"], [6, 5, 1, "", "content_repr"], [6, 5, 1, "", "dump"], [6, 5, 1, "", "dumps"], [6, 5, 1, "", "error"], [6, 5, 1, "", "get_extended_props"], [6, 5, 1, "", "get_props"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"], [6, 5, 1, "", "make_parser"], [6, 5, 1, "", "prop_repr"], [6, 5, 1, "", "quote"], [6, 5, 1, "", "read_content"], [6, 5, 1, "", "read_nodes"], [6, 5, 1, "", "repr_short"], [6, 5, 1, "", "skip_quoted_name"], [6, 5, 1, "", "skip_spaces_and_comments"], [6, 5, 1, "", "unquote"]], "ete4.parser.nexus": [[6, 6, 1, "", "NexusError"], [6, 5, 1, "", "apply_translations"], [6, 5, 1, "", "get_commands"], [6, 5, 1, "", "get_section"], [6, 5, 1, "", "get_sections"], [6, 5, 1, "", "get_trees"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"]], "ete4.phylo": [[7, 0, 1, "", "EvolEvent"]], "ete4.smartview.gui": [[9, 4, 0, "-", "server"]], "ete4.smartview.gui.server": [[9, 0, 1, "", "GlobalStuff"], [9, 0, 1, "", "TreeData"], [9, 5, 1, "", "activate_clade"], [9, 5, 1, "", "activate_node"], [9, 5, 1, "", "add_tree"], [9, 5, 1, "", "add_trees_from_request"], [9, 5, 1, "", "callback"], [9, 5, 1, "", "change_selection_name"], [9, 5, 1, "", "copy_style"], [9, 5, 1, "", "deactivate_clade"], [9, 5, 1, "", "deactivate_node"], [9, 5, 1, "", "del_tree"], [9, 5, 1, "", "find_node"], [9, 5, 1, "", "get_active_clade"], [9, 5, 1, "", "get_active_clades"], [9, 5, 1, "", "get_command_search"], [9, 5, 1, "", "get_drawer"], [9, 5, 1, "", "get_eval_search"], [9, 5, 1, "", "get_layouts"], [9, 5, 1, "", "get_layouts_from_getters"], [9, 5, 1, "", "get_newick"], [9, 5, 1, "", "get_next_available_port"], [9, 5, 1, "", "get_nodes_info"], [9, 5, 1, "", "get_parents"], [9, 5, 1, "", "get_parser"], [9, 5, 1, "", "get_search_function"], [9, 5, 1, "", "get_selection_info"], [9, 5, 1, "", "get_selections"], [9, 5, 1, "", "get_stats"], [9, 5, 1, "", "get_tid"], [9, 5, 1, "", "get_topological_search"], [9, 5, 1, "", "get_trees_from_file"], [9, 5, 1, "", "get_trees_from_form"], [9, 5, 1, "", "get_trees_from_nexus_or_newick"], [9, 5, 1, "", "initialize"], [9, 5, 1, "", "initialize_tree_style"], [9, 5, 1, "", "json_error"], [9, 5, 1, "", "load_tree"], [9, 5, 1, "", "load_tree_from_newick"], [9, 5, 1, "", "maintenance"], [9, 5, 1, "", "make_name"], [9, 5, 1, "", "nice_html"], [9, 5, 1, "", "open_browser_window"], [9, 5, 1, "", "prune_by_selection"], [9, 5, 1, "", "remove_active"], [9, 5, 1, "", "remove_active_clade"], [9, 5, 1, "", "remove_search"], [9, 5, 1, "", "remove_selection"], [9, 5, 1, "", "req_json"], [9, 5, 1, "", "retrieve_layouts"], [9, 5, 1, "", "retrieve_tree_data"], [9, 5, 1, "", "run_smartview"], [9, 5, 1, "", "safer_eval"], [9, 5, 1, "", "search_to_selection"], [9, 5, 1, "", "sort"], [9, 5, 1, "", "store_active"], [9, 5, 1, "", "store_search"], [9, 5, 1, "", "store_selection"], [9, 5, 1, "", "touch_and_get"], [9, 5, 1, "", "unselect_node"], [9, 5, 1, "", "update_app_available_layouts"], [9, 5, 1, "", "update_layouts"], [9, 5, 1, "", "update_node_props"], [9, 5, 1, "", "update_node_style"], [9, 5, 1, "", "update_selection"]], "ete4.smartview.gui.server.TreeData": [[9, 1, 1, "", "__init__"], [9, 3, 1, "", "active"], [9, 3, 1, "", "exclude_props"], [9, 3, 1, "", "include_props"], [9, 3, 1, "", "initialized"], [9, 3, 1, "", "layouts"], [9, 3, 1, "", "name"], [9, 3, 1, "", "nodestyles"], [9, 3, 1, "", "searches"], [9, 3, 1, "", "selected"], [9, 3, 1, "", "style"], [9, 3, 1, "", "timer"], [9, 3, 1, "", "tree"], [9, 3, 1, "", "ultrametric"]], "ete4.smartview.renderer": [[9, 4, 0, "-", "draw_helpers"], [9, 4, 0, "-", "drawer"], [9, 4, 0, "-", "face_positions"], [9, 4, 0, "-", "faces"], [9, 4, 0, "-", "nodestyle"], [9, 4, 0, "-", "treelayout"], [9, 4, 0, "-", "treestyle"]], "ete4.smartview.renderer.draw_helpers": [[9, 0, 1, "", "Box"], [9, 0, 1, "", "Padding"], [9, 5, 1, "", "cartesian"], [9, 5, 1, "", "circumasec"], [9, 5, 1, "", "circumrect"], [9, 5, 1, "", "clip_angles"], [9, 5, 1, "", "draw_arc"], [9, 5, 1, "", "draw_array"], [9, 5, 1, "", "draw_arrow"], [9, 5, 1, "", "draw_circle"], [9, 5, 1, "", "draw_ellipse"], [9, 5, 1, "", "draw_html"], [9, 5, 1, "", "draw_img"], [9, 5, 1, "", "draw_line"], [9, 5, 1, "", "draw_nodebox"], [9, 5, 1, "", "draw_outline"], [9, 5, 1, "", "draw_rect"], [9, 5, 1, "", "draw_rhombus"], [9, 5, 1, "", "draw_slice"], [9, 5, 1, "", "draw_text"], [9, 5, 1, "", "draw_triangle"], [9, 5, 1, "", "first_value"], [9, 5, 1, "", "get_line_type"], [9, 5, 1, "", "get_xs"], [9, 5, 1, "", "get_ys"], [9, 5, 1, "", "intersects_angles"], [9, 5, 1, "", "intersects_box"], [9, 5, 1, "", "intersects_segment"], [9, 5, 1, "", "split_thru_negative_xaxis"], [9, 5, 1, "", "summary"]], "ete4.smartview.renderer.draw_helpers.Box": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"], [9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.draw_helpers.Padding": [[9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.drawer": [[9, 0, 1, "", "Active"], [9, 0, 1, "", "Drawer"], [9, 0, 1, "", "DrawerAlignCircFaces"], [9, 0, 1, "", "DrawerAlignRectFaces"], [9, 0, 1, "", "DrawerCirc"], [9, 0, 1, "", "DrawerCircFaces"], [9, 0, 1, "", "DrawerRect"], [9, 0, 1, "", "DrawerRectFaces"], [9, 0, 1, "", "Size"], [9, 0, 1, "", "TreeActive"], [9, 5, 1, "", "dist"], [9, 5, 1, "", "drawn_size"], [9, 5, 1, "", "get_asec"], [9, 5, 1, "", "get_drawers"], [9, 5, 1, "", "get_empty_active"], [9, 5, 1, "", "get_rect"], [9, 5, 1, "", "make_box"], [9, 5, 1, "", "safe_string"], [9, 5, 1, "", "stack"]], "ete4.smartview.renderer.drawer.Active": [[9, 3, 1, "", "parents"], [9, 3, 1, "", "results"]], "ete4.smartview.renderer.drawer.Drawer": [[9, 3, 1, "", "COLLAPSE_SIZE"], [9, 3, 1, "", "MIN_SIZE"], [9, 3, 1, "", "NPANELS"], [9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "draw_aligned_headers"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_content"], [9, 1, 1, "", "draw_node"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_active_children"], [9, 1, 1, "", "get_collapsed_node"], [9, 1, 1, "", "get_outline"], [9, 1, 1, "", "get_popup_props"], [9, 1, 1, "", "get_selected_children"], [9, 1, 1, "", "is_fully_collapsed"], [9, 1, 1, "", "on_first_visit"], [9, 1, 1, "", "on_last_visit"]], "ete4.smartview.renderer.drawer.DrawerAlignCircFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerAlignRectFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerCirc": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerCircFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.DrawerRect": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerRectFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.Size": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"]], "ete4.smartview.renderer.drawer.TreeActive": [[9, 3, 1, "", "clades"], [9, 3, 1, "", "nodes"]], "ete4.smartview.renderer.face_positions": [[9, 0, 1, "", "AlignedGrid"], [9, 0, 1, "", "Grid"], [9, 5, 1, "", "make_faces"]], "ete4.smartview.renderer.face_positions.AlignedGrid": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.face_positions.Grid": [[9, 1, 1, "", "add_face"]], "ete4.smartview.renderer.faces": [[9, 0, 1, "", "AlignLinkFace"], [9, 0, 1, "", "AlignmentFace"], [9, 0, 1, "", "ArrowFace"], [9, 0, 1, "", "AttrFace"], [9, 0, 1, "", "CircleFace"], [9, 0, 1, "", "Face"], [9, 0, 1, "", "HTMLFace"], [9, 0, 1, "", "ImgFace"], [9, 0, 1, "", "LegendFace"], [9, 0, 1, "", "OutlineFace"], [9, 0, 1, "", "PieChartFace"], [9, 0, 1, "", "RectFace"], [9, 0, 1, "", "ScaleFace"], [9, 0, 1, "", "SelectedCircleFace"], [9, 0, 1, "", "SelectedFace"], [9, 0, 1, "", "SelectedRectFace"], [9, 0, 1, "", "SeqFace"], [9, 0, 1, "", "SeqMotifFace"], [9, 0, 1, "", "StackedBarFace"], [9, 0, 1, "", "TextFace"]], "ete4.smartview.renderer.faces.AlignLinkFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.AlignmentFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_blocks"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "get_seq"]], "ete4.smartview.renderer.faces.ArrowFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 2, 1, "", "orientation"]], "ete4.smartview.renderer.faces.AttrFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_content"]], "ete4.smartview.renderer.faces.CircleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.Face": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "compute_fsize"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "get_content"], [9, 1, 1, "", "in_aligned_viewport"]], "ete4.smartview.renderer.faces.HTMLFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ImgFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.LegendFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.OutlineFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.PieChartFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_pie"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.RectFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ScaleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SelectedCircleFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedRectFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SeqFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SeqMotifFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_regions"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.faces.StackedBarFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.TextFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.layouts": [[9, 4, 0, "-", "context_layouts"], [9, 4, 0, "-", "default_layouts"], [9, 4, 0, "-", "domain_layouts"], [9, 4, 0, "-", "eggnog6_layouts"], [9, 4, 0, "-", "etecompare_layouts"], [9, 4, 0, "-", "evocell_layouts"], [9, 4, 0, "-", "evol_events_layouts"], [9, 4, 0, "-", "ncbi_taxonomy_layouts"], [9, 4, 0, "-", "phylocloud_egg5_layouts"], [9, 4, 0, "-", "seq_layouts"], [9, 4, 0, "-", "spongilla_layouts"], [9, 4, 0, "-", "staple_layouts"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, 0, 1, "", "LayoutGenomicContext"]], "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_context"], [9, 1, 1, "", "get_tooltip"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, 0, 1, "", "LayoutBranchLength"], [9, 0, 1, "", "LayoutBranchSupport"], [9, 0, 1, "", "LayoutLeafName"], [9, 0, 1, "", "LayoutNumberLeaves"], [9, 0, 1, "", "LayoutOutline"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, 0, 1, "", "LayoutBestName"], [9, 0, 1, "", "LayoutBigg"], [9, 0, 1, "", "LayoutCard"], [9, 0, 1, "", "LayoutCazy"], [9, 0, 1, "", "LayoutEvolEvents"], [9, 0, 1, "", "LayoutKeggEnzyme"], [9, 0, 1, "", "LayoutKeggModule"], [9, 0, 1, "", "LayoutKeggNumber"], [9, 0, 1, "", "LayoutKeggPathway"], [9, 0, 1, "", "LayoutLastCommonAncestor"], [9, 0, 1, "", "LayoutPdb"], [9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutProteinName"], [9, 0, 1, "", "LayoutScientificName"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, 0, 1, "", "LayoutEteDiffDistance"]], "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, 0, 1, "", "LayoutHumanOGs"], [9, 0, 1, "", "LayoutUCSC"], [9, 0, 1, "", "LayoutUCSCtrans"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, 0, 1, "", "LayoutEvolEvents"]], "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, 0, 1, "", "LayoutLastCommonAncestor"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, 5, 1, "", "get_layout_evoltype"], [9, 5, 1, "", "get_layout_gnames"], [9, 5, 1, "", "get_layout_lca_rects"], [9, 5, 1, "", "get_layout_ogs_egg5"], [9, 5, 1, "", "get_layout_sciname"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, 0, 1, "", "LayoutAlignment"]], "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_seq"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, 0, 1, "", "LayoutAutoName"], [9, 0, 1, "", "LayoutCuratedName"], [9, 0, 1, "", "LayoutEukOgs"], [9, 0, 1, "", "LayoutPreferredName"], [9, 0, 1, "", "LayoutSciName"], [9, 0, 1, "", "LayoutSeeds"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, 0, 1, "", "LayoutBarplot"]], "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.nodestyle": [[9, 0, 1, "", "NodeStyle"]], "ete4.smartview.renderer.nodestyle.NodeStyle": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "init"]], "ete4.smartview.renderer.treelayout": [[9, 0, 1, "", "TreeLayout"], [9, 5, 1, "", "cased_name"]], "ete4.smartview.renderer.treelayout.TreeLayout": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.treestyle": [[9, 0, 1, "", "TreeStyle"]], "ete4.smartview.renderer.treestyle.TreeStyle": [[9, 1, 1, "", "__init__"], [9, 2, 1, "", "active_face"], [9, 2, 1, "", "active_face_pos"], [9, 1, 1, "", "add_legend"], [9, 2, 1, "", "aligned_panel_footer"], [9, 2, 1, "", "aligned_panel_header"], [9, 1, 1, "", "get_legend"], [9, 2, 1, "", "selected_face"], [9, 2, 1, "", "selected_face_pos"]], "ete4.treematcher": [[12, 4, 0, "-", "treematcher"]], "ete4.treematcher.treematcher": [[12, 0, 1, "", "TreePattern"], [12, 5, 1, "", "match"], [12, 5, 1, "", "safer_eval"], [12, 5, 1, "", "search"]], "ete4.treematcher.treematcher.TreePattern": [[12, 1, 1, "", "__init__"], [12, 1, 1, "", "match"], [12, 1, 1, "", "search"]], "": [[13, 4, 0, "-", "treeview"]]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:property", "3": "py:attribute", "4": "py:module", "5": "py:function", "6": "py:exception"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "property", "Python property"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "module", "Python module"], "5": ["py", "function", "Python function"], "6": ["py", "exception", "Python exception"]}, "titleterms": {"about": 0, "highlight": 0, "tool": 0, "us": [0, 1, 17], "et": [0, 1, 2, 19], "relat": 0, "link": [0, 15], "resourc": 0, "frequent": 1, "ask": 1, "question": 1, "content": [1, 2, 9, 13, 15, 16, 17, 18, 19, 20], "gener": 1, "how": [1, 19], "do": 1, "i": 1, "tree": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "brows": [1, 19], "find": [1, 19], "leaf": [1, 16, 20], "its": 1, "name": [1, 16, 20], "visit": 1, "all": [1, 19], "node": [1, 15, 16, 18, 19, 20], "within": [1, 19, 20], "can": 1, "control": [1, 15, 16], "order": 1, "which": 1, "ar": 1, "read": [1, 19], "write": [1, 19], "load": 1, "intern": 1, "support": [1, 16, 20], "export": 1, "annot": [1, 16, 17, 19], "newick": [1, 6, 19], "format": 1, "visual": [1, 15, 16, 20], "draw": [1, 9, 16, 20], "circular": [1, 20], "imag": [1, 20], "svg": 1, "veri": 1, "unbalanc": 1, "branch": [1, 16, 19, 20], "improv": 1, "welcom": 2, "": [2, 16, 19], "document": 2, "indic": 2, "tabl": 2, "refer": 3, "guid": 3, "cluster": 4, "oper": [5, 19], "parser": 6, "nexu": 6, "phylogenet": [7, 15, 20], "phylotre": 7, "evolev": 7, "multipl": [8, 15, 16], "sequenc": [8, 15, 16, 20], "align": [8, 15, 16], "seqgroup": 8, "smartview": 9, "web": [9, 16], "graphic": [9, 13], "server": 9, "render": [9, 20], "drawer": 9, "helper": 9, "face": [9, 13, 16, 20], "posit": [9, 16, 20], "nodestyl": [9, 13], "treelayout": 9, "treestyl": [9, 13], "layout": [9, 16, 20], "context": 9, "default": 9, "domain": [9, 16, 20], "eggnog6": 9, "etecompar": 9, "evocel": 9, "evol_ev": 9, "ncbi_taxonomi": 9, "phylocloud_egg5": 9, "seq": 9, "spongilla": 9, "stapl": 9, "taxonomi": [10, 17], "databas": [10, 17], "ncbitaxa": 10, "gtdbtaxa": 10, "main": 11, "class": 11, "matcher": [12, 18], "treeview": 13, "qt": [13, 20], "tutori": 14, "overview": [15, 16, 17, 20], "ad": 15, "taxonom": 15, "inform": [15, 17], "automat": [15, 17], "speci": [15, 17], "info": 15, "custom": [15, 16, 19, 20], "manual": 15, "detect": 15, "evolutionari": 15, "event": 15, "overlap": 15, "so": 15, "algorithm": 15, "reconcili": 15, "A": [15, 18], "closer": 15, "look": 15, "object": [15, 16], "rel": [15, 19], "date": 15, "implement": 15, "root": [15, 19], "outgroup": [15, 19], "work": [15, 19], "duplic": [15, 19], "gene": 15, "famili": 15, "treeko": 15, "split": 15, "collaps": [15, 16, 19], "specif": 15, "explor": 16, "interact": [16, 20], "standalon": 16, "script": 16, "session": 16, "verbos": 16, "mode": 16, "show": [16, 20], "length": [16, 20], "properti": [16, 19, 20], "pop": 16, "up": [16, 17], "panel": 16, "1": 16, "tab": 16, "overral": 16, "download": 16, "2": 16, "search": [16, 19], "select": 16, "simpl": [16, 18], "regular": 16, "express": [16, 18], "topolog": 16, "exampl": [16, 18], "possibl": 16, "match": [16, 19], "3": 16, "advanc": [16, 19], "aspect": [16, 20], "style": [16, 20], "add": [16, 20], "legend": [16, 20], "clade": 16, "function": [16, 19, 20], "combin": [16, 20], "fix": [16, 20], "defin": 16, "background": [16, 20], "color": 16, "strip": 16, "outlin": 16, "bar": 16, "plot": 16, "heatmap": 16, "differ": 17, "between": [17, 19, 20], "ncbi": 17, "gtdb": 17, "ete4": 17, "set": 17, "local": 17, "copi": [17, 19], "get": [17, 19], "taxid": 17, "descend": [17, 19], "taxa": 17, "topologi": [17, 18, 19], "onli": 18, "less": 18, "outsid": 18, "variabl": 18, "from": [18, 19], "test": 18, "suit": 18, "structur": 19, "creat": [19, 20], "understand": 19, "basic": 19, "attribut": 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"]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest"]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant"]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit"]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back"]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches"]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate"]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references"]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch"]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize"]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name"]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint"]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move"]], "node (walker property)": [[5, "ete4.core.operations.Walker.node"]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id"]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate"]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform"]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule"]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang"]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove"]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy"]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at"]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup"]], "set_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_outgroup"]], "sort() (in module ete4.core.operations)": [[5, "ete4.core.operations.sort"]], "swap_props() (in module ete4.core.operations)": [[5, "ete4.core.operations.swap_props"]], "to_dendrogram() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_dendrogram"]], "to_ultrametric() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_ultrametric"]], "traverse() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse"]], "traverse_bfs() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse_bfs"]], "unroot() (in module ete4.core.operations)": [[5, "ete4.core.operations.unroot"]], "update_size() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_size"]], "update_sizes_all() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_all"]], "update_sizes_from() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_from"]], "walk() (in module ete4.core.operations)": [[5, "ete4.core.operations.walk"]], "newickerror": [[6, "ete4.parser.newick.NewickError"]], "nexuserror": [[6, "ete4.parser.nexus.NexusError"]], "apply_translations() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.apply_translations"]], "content_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.content_repr"]], "dump() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dump"]], "dumps() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dumps"]], "error() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.error"]], "ete4.parser.newick": [[6, "module-ete4.parser.newick"]], "ete4.parser.nexus": [[6, "module-ete4.parser.nexus"]], "get_commands() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_commands"]], "get_extended_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_extended_props"]], "get_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_props"]], "get_section() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_section"]], "get_sections() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_sections"]], "get_trees() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_trees"]], "load() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.load"]], "load() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.load"]], "loads() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.loads"]], "loads() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.loads"]], "make_parser() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.make_parser"]], "prop_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.prop_repr"]], "quote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.quote"]], "read_content() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_content"]], "read_nodes() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_nodes"]], "repr_short() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.repr_short"]], "skip_quoted_name() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_quoted_name"]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_spaces_and_comments"]], "unquote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.unquote"]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree"]], "__init__() (phylotree method)": [[7, "ete4.PhyloTree.__init__"]], "annotate_gtdb_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[7, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[7, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[7, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries"]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq"]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries"]], "set_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.set_seq"]], "write() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.write"]], "active (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Active"]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace"]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid"]], "alignmentface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignmentFace"]], "arrowface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ArrowFace"]], "attrface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AttrFace"]], "box (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Box"]], "collapse_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE"]], "circleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.CircleFace"]], "drawer (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Drawer"]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces"]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces"]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc"]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces"]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRect"]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces"]], "face (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.Face"]], "globalstuff (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.GlobalStuff"]], "grid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.Grid"]], "htmlface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.HTMLFace"]], "imgface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ImgFace"]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment"]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName"]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot"]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName"]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg"]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength"]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport"]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard"]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy"]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName"]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance"]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs"]], "layoutevolevents (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents"]], "layoutevolevents (class in ete4.smartview.renderer.layouts.evol_events_layouts)": [[9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents"]], "layoutgenomiccontext (class in ete4.smartview.renderer.layouts.context_layouts)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext"]], "layouthumanogs (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs"]], "layoutkeggenzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme"]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule"]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber"]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway"]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor"]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor"]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName"]], "layoutnumberleaves (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves"]], "layoutoutline (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline"]], "layoutpdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb"]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains"]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains"]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName"]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName"]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName"]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName"]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains"]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC"]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans"]], "legendface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.LegendFace"]], "min_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE"]], "npanels (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.NPANELS"]], "npanels (draweraligncircfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS"]], "npanels (draweralignrectfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS"]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle"]], "outlineface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.OutlineFace"]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Padding"]], "piechartface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.PieChartFace"]], "rectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.RectFace"]], "scaleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ScaleFace"]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace"]], "selectedface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedFace"]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace"]], "seqface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqFace"]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace"]], "size (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Size"]], "stackedbarface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.StackedBarFace"]], "type (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.TYPE"]], "type (drawercirc attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.TYPE"]], "type (drawerrect attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.TYPE"]], "textface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.TextFace"]], "treeactive (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.TreeActive"]], "treedata (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.TreeData"]], "treelayout (class in ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout"]], "treestyle (class in ete4.smartview.renderer.treestyle)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle"]], "__init__() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.__init__"]], "__init__() (alignedgrid method)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid.__init__"]], "__init__() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.__init__"]], "__init__() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.__init__"]], "__init__() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.__init__"]], "__init__() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.__init__"]], "__init__() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.__init__"]], "__init__() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.__init__"]], "__init__() (face method)": [[9, "ete4.smartview.renderer.faces.Face.__init__"]], "__init__() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.__init__"]], "__init__() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.__init__"]], "__init__() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.__init__"]], "__init__() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.__init__"]], "__init__() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.__init__"]], "__init__() (layoutbestname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName.__init__"]], "__init__() (layoutbigg method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg.__init__"]], "__init__() (layoutbranchlength method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength.__init__"]], "__init__() (layoutbranchsupport method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport.__init__"]], "__init__() (layoutcard method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard.__init__"]], "__init__() (layoutcazy method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy.__init__"]], "__init__() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.__init__"]], "__init__() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.__init__"]], "__init__() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.__init__"]], "__init__() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.__init__"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.__init__"]], "__init__() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.__init__"]], "__init__() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.__init__"]], "__init__() (layoutkeggenzyme method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme.__init__"]], "__init__() (layoutkeggmodule method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule.__init__"]], "__init__() (layoutkeggnumber method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber.__init__"]], "__init__() (layoutkeggpathway method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway.__init__"]], "__init__() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.__init__"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.__init__"]], "__init__() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.__init__"]], "__init__() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.__init__"]], "__init__() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.__init__"]], "__init__() (layoutpdb method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb.__init__"]], "__init__() (layoutpfamdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains.__init__"]], "__init__() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.__init__"]], "__init__() (layoutproteinname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName.__init__"]], "__init__() (layoutsciname method)": [[9, "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, "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_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"]], "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_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data"]], "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, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop"]], "delete() (tree method)": [[11, "ete4.Tree.delete"]], "descendants() (tree method)": [[11, "ete4.Tree.descendants"]], "describe() (tree method)": [[11, "ete4.Tree.describe"]], "detach() (tree method)": [[11, "ete4.Tree.detach"]], "dist (tree attribute)": [[11, "ete4.Tree.dist"]], "edges() (tree method)": [[11, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies"]], "explore() (tree method)": [[11, "ete4.Tree.explore"]], "faces (tree attribute)": [[11, "ete4.Tree.faces"]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table"]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio"]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content"]], "get_children() (tree method)": [[11, "ete4.Tree.get_children"]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf"]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance"]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf"]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node"]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup"]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic"]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop"]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters"]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id"]], "id (tree attribute)": [[11, "ete4.Tree.id"]], "img_style (tree property)": [[11, "ete4.Tree.img_style"]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete"]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick"]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed"]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized"]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf"]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic"]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root"]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder"]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize"]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names"]], "leaves() (tree method)": [[11, "ete4.Tree.leaves"]], "level (tree attribute)": [[11, "ete4.Tree.level"]], "lineage() (tree method)": [[11, "ete4.Tree.lineage"]], "name (tree attribute)": [[11, "ete4.Tree.name"]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child"]], "populate() (tree method)": [[11, "ete4.Tree.populate"]], "props (tree attribute)": [[11, "ete4.Tree.props"]], "prune() (tree method)": [[11, "ete4.Tree.prune"]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child"]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children"]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister"]], "render() (tree method)": [[11, "ete4.Tree.render"]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy"]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children"]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds"]], "root (tree attribute)": [[11, "ete4.Tree.root"]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors"]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants"]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name"]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes"]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup"]], "set_style() (tree method)": [[11, "ete4.Tree.set_style"]], "show() (tree method)": [[11, "ete4.Tree.show"]], "size (tree attribute)": [[11, "ete4.Tree.size"]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style"]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants"]], "standardize() (tree method)": [[11, "ete4.Tree.standardize"]], "support (tree attribute)": [[11, "ete4.Tree.support"]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children"]], "to_str() (tree method)": [[11, "ete4.Tree.to_str"]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric"]], "traverse() (tree method)": [[11, "ete4.Tree.traverse"]], "unroot() (tree method)": [[11, "ete4.Tree.unroot"]], "up (tree attribute)": [[11, "ete4.Tree.up"]], "write() (tree method)": [[11, "ete4.Tree.write"]], "treepattern (class in ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.TreePattern"]], "__init__() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.__init__"]], "ete4.treematcher.treematcher": [[12, "module-ete4.treematcher.treematcher"]], "match() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.match"]], "match() (in module ete4.treematcher.treematcher)": [[12, "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
+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", "reference/reference_smartview.rst", "reference/reference_taxonomy.rst", "reference/reference_tree.rst", "reference/reference_treematcher.rst", "reference/reference_treeview.rst", "tutorial/index.rst", "tutorial/tutorial_phylogeny.rst", "tutorial/tutorial_smartview.rst", "tutorial/tutorial_taxonomy.rst", "tutorial/tutorial_treematcher.rst", "tutorial/tutorial_trees.rst", "tutorial/tutorial_treeview.rst"], "titles": ["About", "Frequently Asked Questions", "Welcome to ETE\u2019s documentation!", "Reference Guide", "Clustering", "Tree operations", "Parsers", "Phylogenetic trees", "Multiple Sequence Alignments (SeqGroup)", "Smartview (web graphics)", "Taxonomy databases", "Tree (main class)", "Tree matcher", "Treeview (qt graphics)", "Tutorial", "Phylogenetic trees", "Tree drawing and exploration (web)", "Taxonomy databases", "Tree matcher", "Working with the Tree structure", "Tree drawing (Qt)"], "terms": {"The": [0, 1, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 20], "toolkit": [0, 17, 19, 20], "wa": [0, 5, 6, 19, 20], "origin": [0, 5, 7, 11, 15, 16, 17, 19, 20], "develop": 0, "bioinformat": [0, 7, 19], "depart": 0, "cipf": 0, "valencia": 0, "spain": 0, "greatli": 0, "improv": [0, 15], "compar": [0, 11, 14, 15], "genom": [0, 7, 9, 15, 17], "group": [0, 7, 10, 11, 15, 19], "crg": 0, "barcelona": 0, "structur": [0, 2, 4, 7, 11, 14, 15, 16, 18, 20], "comput": [0, 4, 9, 11, 19], "biologi": [0, 15], "unit": [0, 11, 20], "embl": 0, "heidelberg": 0, "germani": 0, "At": 0, "present": [0, 1, 7, 9, 10, 11, 15, 19], "i": [0, 4, 5, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "maintain": [0, 20], "metagenom": 0, "cbgp": 0, "madrid": 0, "citat": [0, 4, 7, 17], "3": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "reconstruct": 0, "analysi": [0, 4, 15, 16, 19, 20], "visual": [0, 2, 11, 14, 19], "phylogenom": 0, "data": [0, 4, 9, 11, 15, 16, 17, 19, 20], "jaim": 0, "huerta": [0, 7, 15], "cepa": [0, 7, 15], "francoi": 0, "serra": 0, "peer": 0, "bork": 0, "mol": 0, "biol": [0, 7], "evol": 0, "2016": 0, "doi": 0, "10": [0, 1, 8, 9, 16, 18, 19, 20], "1093": 0, "molbev": 0, "msw046": 0, "support": [0, 5, 6, 8, 9, 11, 18, 19], "etetoolkit": [0, 17], "googlegroup": 0, "com": [0, 11, 16, 17], "contact": 0, "jhcepa": [0, 11], "gmail": 0, "eggnog": 0, "orthologi": [0, 15], "databas": [0, 2, 3, 7, 14], "phylomedb": 0, "phylogenet": [0, 1, 2, 3, 5, 11, 14, 19], "polyphoni": 0, "3d": 0, "compars": 0, "phylemon": 0, "speci": [0, 1, 7, 10, 11, 14, 16, 18, 19, 20], "delimit": 0, "method": [0, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "treeko": [0, 7, 19], "duplic": [0, 1, 7, 11, 14], "awar": [0, 15], "tree": [0, 2, 3, 4, 6, 9, 10, 14], "agp": 0, "align": [0, 2, 3, 7, 9, 11, 14, 20], "free": [0, 18], "phylogeni": [0, 15], "itep": 0, "explor": [0, 1, 2, 9, 11, 14, 15, 19, 20], "microbi": 0, "pan": [0, 15, 17, 20], "t": [0, 1, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "rmsd": 0, "protein": [0, 9], "classif": [0, 17], "cansnper": 0, "genotyp": 0, "classifi": 0, "clonal": 0, "pathogen": 0, "reprophylo": 0, "reproduc": [0, 11, 20], "analys": [0, 15, 19, 20], "avocado": 0, "linux": 0, "autom": [0, 19], "test": [0, 14], "streptomedb": 0, "2": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "0": [0, 1, 4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "natur": [0, 19], "product": 0, "produc": [0, 5, 11, 18, 19], "streptomycet": 0, "iq": 0, "web": [0, 2, 3, 14, 17], "server": [0, 3, 11, 16, 17], "fast": [0, 19], "accur": 0, "under": [0, 4, 10, 11, 15, 16, 19], "maximum": [0, 8, 9, 19], "likelihood": 0, "A": [0, 1, 4, 5, 7, 10, 11, 12, 14, 16, 17, 19, 20], "brief": 0, "introduct": 0, "its": [0, 5, 6, 7, 9, 10, 11, 15, 16, 17, 19, 20], "programmat": 0, "featur": [0, 1, 4, 7, 11, 15, 16, 17, 19, 20], "scipi": 0, "confer": 0, "2015": 0, "littl": 0, "comparison": [0, 15, 19], "how": [0, 4, 11, 15, 16, 18, 20], "handl": [0, 19, 20], "r": [0, 6, 9, 15, 16, 19], "v": [0, 16, 20], "python": [0, 1, 11, 12, 15, 16, 18, 19, 20], "climateecologi": 0, "blog": 0, "sever": [0, 1, 11, 15, 16, 17, 18, 19, 20], "wai": [0, 1, 11, 15, 17, 18, 19, 20], "displai": 0, "associ": [0, 4, 7, 8, 10, 11, 15, 17], "bacpathgenom": 0, "pars": [0, 4, 7, 10, 11, 15, 17, 19], "list": [0, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 20], "word": [0, 10, 15, 19], "build": [0, 9], "trie": 0, "stackoverflow": 0, "annot": [0, 7, 10, 14], "holt": 0, "lab": 0, "script": [0, 1, 17], "guid": [0, 2], "ete3": [0, 16], "api": [0, 9], "exampl": [0, 1, 4, 5, 6, 7, 8, 9, 11, 14, 15, 17, 19, 20], "e": [0, 1, 5, 9, 10, 11, 16, 18, 19, 20], "noutahi": 0, "plot": [0, 20], "avrilom": 0, "includ": [1, 5, 7, 8, 15, 16, 17, 18, 19, 20], "basic": [1, 7, 14, 15, 16, 20], "standalon": [1, 15], "program": [1, 16, 18, 19, 20], "quickli": [1, 18, 19], "your": [1, 15, 16, 17, 19], "type": [1, 9, 11, 15, 16, 19, 20], "ete4": [1, 9, 11, 14, 15, 16, 18, 19, 20], "file": [1, 4, 6, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "termin": [1, 11, 15, 16, 19, 20], "run": [1, 16, 18], "For": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "instanc": [1, 7, 10, 11, 15, 16, 17, 19, 20], "mytreefil": 1, "nw": [1, 4, 9, 11, 15, 16, 19, 20], "simpl": [1, 4, 14, 15, 17, 19, 20], "implement": [1, 7, 19, 20], "doe": [1, 10, 12, 15, 17, 18, 19, 20], "allow": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "fanci": 1, "custom": [1, 10, 11, 14, 17], "howev": [1, 15, 17, 19, 20], "more": [1, 5, 7, 11, 15, 16, 18, 19, 20], "than": [1, 5, 11, 15, 16, 17, 19, 20], "main": [1, 2, 3, 9, 16, 17, 18, 19, 20], "goal": 1, "provid": [1, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "librari": 1, "so": [1, 5, 7, 11, 16, 17, 18, 19], "you": [1, 7, 8, 15, 16, 17, 19, 20], "creat": [1, 4, 5, 9, 11, 12, 15, 16], "own": [1, 15, 16, 19, 20], "manipul": [1, 16, 19, 20], "shell": 1, "could": [1, 4, 11, 15, 16, 18, 19, 20], "from": [1, 5, 6, 7, 9, 10, 11, 14, 15, 16, 17, 20], "import": [1, 5, 11, 15, 16, 17, 18, 19, 20], "t1": [1, 4, 11, 19], "b": [1, 4, 5, 11, 16, 17, 18, 19, 20], "c": [1, 4, 5, 11, 16, 18, 19, 20], "string": [1, 4, 7, 8, 11, 12, 15, 19], "t2": [1, 4, 11, 15, 19], "open": [1, 4, 9, 10, 11, 16, 19], "mani": [1, 7, 9, 11, 15, 19, 20], "tutori": [1, 2], "follow": [1, 4, 7, 11, 15, 16, 17, 19, 20], "shortcut": [1, 16, 18], "note": [1, 7, 11, 15, 16, 17, 18, 19, 20], "assum": [1, 7, 19], "tip1": 1, "There": [1, 11, 15, 18, 19, 20], "thi": [1, 4, 5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "easiest": [1, 17], "one": [1, 4, 7, 9, 11, 15, 16, 17, 18, 19, 20], "travers": [1, 3, 5, 11, 14, 18, 20], "print": [1, 5, 8, 11, 15, 16, 17, 18, 19], "ye": [1, 15, 18], "current": [1, 5, 7, 8, 9, 10, 11, 15, 16, 19], "strategi": [1, 11, 12, 17, 19], "pre": [1, 5, 10, 11, 16, 19, 20], "post": [1, 5, 9, 11, 19], "level": [1, 5, 10, 11, 15, 16, 19], "over": [1, 7, 8, 11, 15, 18, 19, 20], "check": [1, 11, 14, 15, 16, 18, 20], "differ": [1, 7, 9, 11, 14, 15, 16, 18, 19, 20], "http": [1, 11, 16, 17, 19], "packag": [1, 15, 17], "org": [1, 11, 19], "tutorial_tre": 1, "html": [1, 9], "slightli": [1, 19], "across": 1, "subformat": 1, "label": [1, 7, 9, 15, 16, 17, 19, 20], "descript": [1, 4, 9, 11, 16, 19, 20], "flexibl": [1, 19], "d": [1, 4, 5, 7, 9, 11, 15, 16, 18, 19, 20], "7": [1, 9, 11, 16, 19], "f": [1, 5, 11, 15, 16, 18, 19, 20], "5": [1, 4, 9, 11, 15, 16, 18, 19, 20], "1": [1, 4, 5, 6, 7, 9, 10, 11, 12, 15, 17, 18, 19, 20], "6": [1, 7, 9, 11, 16, 19, 20], "h": [1, 7, 11, 15, 16, 18, 19, 20], "8": [1, 7, 9, 11, 16, 19, 20], "w": [1, 11, 16, 19, 20], "length": [1, 6, 9, 11, 15, 19], "4": [1, 9, 11, 15, 18, 19, 20], "leav": [1, 4, 5, 7, 9, 11, 15, 16, 17, 18, 20], "onli": [1, 5, 7, 9, 11, 14, 15, 16, 17, 19, 20], "9": [1, 9, 10, 11, 15, 16, 19], "100": [1, 11, 16, 19, 20], "topologi": [1, 5, 7, 11, 14, 15, 16, 20], "In": [1, 11, 15, 16, 17, 18, 19, 20], "specifi": [1, 4, 9, 11, 15, 19], "parser": [1, 2, 3, 4, 7, 9, 11, 12, 15, 18, 19], "my_tre": 1, "when": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "default": [1, 4, 6, 7, 11, 15, 16, 17, 19, 20], "": [1, 4, 6, 7, 9, 10, 11, 12, 15, 18, 20], "distanc": [1, 4, 5, 9, 11, 14, 15], "depend": [1, 5, 11, 15, 19, 20], "If": [1, 5, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "want": [1, 5, 11, 16, 18, 19, 20], "save": [1, 9, 15, 16, 19, 20], "other": [1, 5, 7, 11, 12, 15, 16, 17, 19, 20], "properti": [1, 4, 5, 6, 7, 9, 10, 11, 14, 15, 17], "need": [1, 6, 9, 10, 12, 15, 16, 19, 20], "them": [1, 5, 8, 10, 11, 15, 16, 18, 19, 20], "call": [1, 9, 11, 12, 15, 16, 17, 18, 19, 20], "prop": [1, 5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "size": [1, 5, 7, 9, 10, 11, 16, 19, 20], "none": [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "start": [1, 5, 6, 9, 11, 16, 18, 19, 20], "version": [1, 7, 9, 12, 15, 17, 19], "render": [1, 3, 11, 14, 15, 16], "mode": [1, 20], "automat": [1, 7, 9, 11, 14, 18, 19, 20], "detect": [1, 7, 11, 14, 17, 19], "filenam": [1, 9], "extens": [1, 11, 15, 20], "code": [1, 5, 7, 9, 11, 12, 15, 16, 17, 19, 20], "vector": [1, 20], "mytre": [1, 20], "chang": [1, 5, 6, 11, 15, 16, 18, 19], "layout": [1, 11, 14, 15], "By": [1, 4, 7, 15, 16, 19], "function": [1, 4, 5, 7, 9, 11, 15, 17, 18], "abl": [1, 16, 18, 19], "add": [1, 4, 5, 7, 8, 9, 10, 11, 17, 19], "remov": [1, 3, 5, 9, 11], "modifi": [1, 14, 16, 20], "almost": 1, "ani": [1, 5, 6, 9, 10, 11, 15, 16, 17, 18, 19, 20], "element": [1, 9, 11, 16, 19, 20], "face": [1, 3, 11, 14], "attrfac": [1, 9, 20], "treestyl": [1, 3, 11, 15, 16, 20], "def": [1, 7, 15, 16, 19, 20], "my_layout": 1, "is_leaf": [1, 6, 11, 16, 18, 19, 20], "name_fac": 1, "els": [1, 16, 17, 19, 20], "fsize": [1, 20], "small": [1, 16, 19, 20], "font": 1, "prefer": [1, 9, 15], "posit": [1, 5, 6, 11, 18, 19], "add_face_to_nod": [1, 20], "column": [1, 9, 11, 16, 20], "right": [1, 9, 11, 16, 19, 20], "show_leaf_nam": [1, 11, 16, 20], "fals": [1, 5, 7, 9, 10, 11, 12, 15, 16, 19, 20], "again": [1, 15, 18, 19], "layout_fn": [1, 20], "g": [1, 6, 11, 16, 18, 19, 20], "m1_t1": 1, "m_1_t2": 1, "m2_t3": 1, "m2_t1": 1, "m2_t2": 1, "show": [1, 9, 11, 15, 19], "tree_styl": [1, 9, 11, 15, 16, 20], "style": [1, 9, 11, 14], "experi": 1, "extrem": 1, "convert": [1, 5, 7, 10, 11, 15, 17, 19], "ultrametr": [1, 5, 9, 11, 16], "make": [1, 5, 11, 16, 17, 18, 19, 20], "end": [1, 6, 9, 11, 16, 18, 19, 20], "same": [1, 7, 9, 11, 15, 16, 17, 18, 19, 20], "popul": [1, 3, 5, 11, 16, 19, 20], "50": [1, 6, 16, 19, 20], "random_branch": [1, 16, 20], "true": [1, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 19, 20], "to_ultrametr": [1, 3, 5, 11], "enabl": [1, 16], "force_topologi": 1, "option": [1, 7, 12, 16, 18, 19, 20], "seen": [1, 7, 11, 19], "engin": [1, 15, 16, 20], "case": [1, 11, 15, 16, 19, 20], "actual": [1, 19], "about": [2, 7, 9, 15, 16, 18, 19, 20], "highlight": [2, 16, 20], "tool": [2, 19], "us": [2, 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 19, 20], "relat": [2, 5, 11, 17, 18, 19], "link": [2, 4, 7, 14, 16, 19, 20], "resourc": [2, 17], "work": [2, 7, 14, 20], "draw": [2, 11, 14, 15], "qt": [2, 3, 14], "taxonomi": [2, 3, 7, 14], "matcher": [2, 3, 14], "refer": [2, 5, 7, 11, 15, 16, 17, 19, 20], "class": [2, 3, 4, 5, 7, 8, 9, 10, 12, 15, 16, 17, 18, 19, 20], "oper": [2, 3, 8, 11, 14, 20], "cluster": [2, 3, 19], "multipl": [2, 3, 7, 14, 17], "sequenc": [2, 3, 5, 7, 9, 11, 14], "seqgroup": [2, 3, 15], "smartview": [2, 3, 11, 16], "graphic": [2, 3, 4, 16, 19, 20], "treeview": [2, 3, 20], "frequent": [2, 19], "ask": [2, 15], "question": 2, "gener": [2, 5, 11, 15, 16, 19, 20], "brows": [2, 14], "read": [2, 6, 7, 9, 14, 15, 16, 20], "write": [2, 7, 8, 11, 14, 15, 16, 18], "index": [2, 4, 5], "modul": [2, 8, 9, 12, 16, 17, 18, 19, 20], "search": [2, 3, 5, 9, 11, 12, 18], "page": [2, 15, 16, 20], "walker": [3, 5], "add_branch_valu": [3, 5], "add_leaf_nam": [3, 5], "assert_root_consist": [3, 5], "common_ancestor": [3, 5, 11, 15, 16, 19, 20], "create_dichotomic_sist": [3, 5], "farthest": [3, 5, 7, 11, 15, 19], "farthest_descend": [3, 5], "insert_intermedi": [3, 5], "interchange_refer": [3, 5], "join_branch": [3, 5], "ladder": [3, 5, 11], "make_nam": [3, 5, 9], "midpoint": [3, 5, 14], "move": [3, 5], "populate_uniform": [3, 5], "populate_yul": [3, 5], "rehang": [3, 5], "resolve_polytomi": [3, 5, 11, 19], "root_at": [3, 5], "set_midpoint_outgroup": [3, 5], "set_outgroup": [3, 5, 11, 19], "sort": [3, 5, 9, 10, 11, 20], "swap_prop": [3, 5], "to_dendrogram": [3, 5], "traverse_bf": [3, 5], "unroot": [3, 5, 11], "update_s": [3, 5], "update_sizes_al": [3, 5], "update_sizes_from": [3, 5], "walk": [3, 5], "newick": [3, 4, 7, 9, 11, 12, 14, 15, 16, 17, 18], "nexu": 3, "phylotre": [3, 10, 15, 17, 18, 19], "evolev": [3, 15], "clustertre": [3, 4], "ncbitaxa": [3, 17], "gtdbtaxa": [3, 17], "nodestyl": [3, 16, 20], "treepattern": [3, 12, 18], "match": [3, 4, 7, 9, 10, 11, 12, 15, 18], "safer_ev": [3, 9, 12], "children": [4, 5, 7, 9, 11, 12, 16, 18, 19, 20], "text_arrai": 4, "fdist": 4, "spearman_dist": 4, "sourc": [4, 6, 7, 8, 9, 10, 12, 16, 19, 20], "base": [4, 7, 9, 11, 15, 17, 19, 20], "repres": [4, 5, 6, 9, 10, 11, 15, 16, 17, 19, 20], "result": [4, 5, 8, 9, 10, 11, 15, 18, 19], "__init__": [4, 7, 8, 9, 10, 11, 12, 16, 20], "paramet": [4, 5, 7, 8, 9, 10, 11, 12, 16, 20], "object": [4, 6, 7, 9, 11, 19, 20], "dict": [4, 6, 9, 10, 11, 16], "content": [4, 6, 7, 11, 14], "singl": [4, 7, 10, 11, 15, 16, 19, 20], "node": [4, 5, 6, 7, 9, 10, 11, 12, 14, 17], "It": [4, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "can": [4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "number": [4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "format": [4, 6, 7, 8, 9, 10, 11, 15, 17, 19, 20], "fine": [4, 11], "grain": [4, 11], "interpret": [4, 9, 11, 15, 16, 19], "see": [4, 7, 9, 11, 15, 16, 18, 19, 20], "pyx": [4, 11], "empti": [4, 11, 15, 17, 19, 20], "name": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 17, 18, 19], "t3": [4, 11, 19], "t4": [4, 11], "home": [4, 11], "user": [4, 11, 16, 17, 19, 20], "my": [4, 11, 16, 20], "deviat": 4, "get_dunn": 4, "calcul": [4, 7, 10, 11, 15, 19], "dunn": 4, "given": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 20], "set": [4, 5, 7, 8, 9, 10, 11, 14, 15, 16, 19, 20], "descend": [4, 5, 7, 10, 11, 14, 16, 18], "get_silhouett": 4, "silhouett": 4, "valu": [4, 5, 7, 9, 11, 15, 16, 17, 18, 19, 20], "euclidean": 4, "also": [4, 7, 9, 10, 11, 15, 17, 18, 19, 20], "profil": [4, 20], "mean": [4, 15, 16, 20], "inter": 4, "intra": 4, "analyz": [4, 19], "intraclust": 4, "interclust": 4, "silhouet": 4, "ar": [4, 7, 8, 10, 11, 12, 15, 16, 17, 18, 19, 20], "centroid": 4, "diamet": [4, 5, 16, 20], "linkag": 4, "rousseeuw": 4, "p": [4, 15, 16, 18, 19], "j": [4, 7, 11, 18, 19], "1987": 4, "aid": 4, "valid": [4, 5, 7, 9, 10, 11, 19], "appl": 4, "math": [4, 16], "20": [4, 9, 16, 20], "53": 4, "65": [4, 16, 20], "intercluster_dist": 4, "intracluster_dist": 4, "leaf_profil": 4, "yield": [4, 5, 9, 11, 12, 18, 19], "link_to_arrayt": 4, "arraytbl": 4, "arrayt": 4, "return": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19, 20], "been": [4, 15], "found": [4, 7, 15, 16, 18, 19, 20], "row": [4, 9, 11], "expect": [4, 7, 15, 18, 19], "leaf": [4, 5, 6, 7, 9, 10, 11, 15, 17, 18, 19], "set_distance_funct": 4, "fn": [4, 7], "silouett": 4, "acept": 4, "two": [4, 5, 11, 15, 16, 18, 19, 20], "numpi": [4, 16], "arrai": [4, 9, 11, 16], "argument": [4, 6, 7, 10, 15, 16, 19, 20], "my_dist_fn": 4, "lambda": [4, 11, 15, 17, 19], "x": [4, 6, 9, 11, 16, 18], "y": [4, 6, 9, 11, 16, 18, 19], "ab": [4, 16, 19], "root": [5, 7, 11, 14, 16, 17, 18, 20], "branch": [5, 9, 10, 11, 14, 15], "prun": 5, "add_next_branch": 5, "self": [5, 7, 9, 11, 16, 19, 20], "first_visit": 5, "go_back": 5, "has_unvisited_branch": 5, "node_id": [5, 9, 11], "dist_fn": [5, 11], "support_fn": [5, 11], "bprop": [5, 11], "rais": [5, 11, 19], "assertionerror": 5, "look": [5, 18, 19], "inconsist": 5, "last": [5, 9, 11, 19], "common": [5, 7, 9, 10, 11, 15, 16, 18, 20], "lineag": [5, 7, 10, 11, 15, 17], "don": 5, "have": [5, 10, 11, 15, 16, 18, 19], "ancestor": [5, 9, 10, 11, 16], "whose": [5, 16, 19, 20], "we": [5, 9, 11, 15, 16, 17, 18, 19, 20], "find": [5, 11, 15, 16, 18], "dichotomi": 5, "old": [5, 11], "new": [5, 7, 9, 11, 15, 16, 18, 19], "sister": [5, 11, 19], "topolog": [5, 7, 11, 15, 18, 19], "intermedi": [5, 11, 17], "dist": [5, 6, 9, 11, 16, 18, 19, 20], "insert": 5, "between": [5, 7, 11, 14, 15, 16], "parent": [5, 9, 10, 11, 16, 18, 19], "an": [5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "node1": [5, 11, 19], "node2": [5, 11, 19], "interchang": 5, "point": [5, 9, 11, 15, 17, 19], "where": [5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "viceversa": 5, "substitut": [5, 15, 18], "child": [5, 7, 10, 11, 19], "revers": [5, 9, 11], "accord": [5, 6, 7, 9, 11, 15, 19, 20], "each": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "partit": [5, 7, 11, 15, 19], "instead": [5, 11, 18, 19, 20], "sum": [5, 11, 19], "lenght": [5, 11, 19], "biggest": 5, "first": [5, 7, 9, 10, 11, 15, 16, 17, 18, 20], "char": [5, 8], "abcdefghijklmnopqrstuvwxyz": 5, "short": [5, 11, 18], "correspond": [5, 6, 7, 9, 10, 15, 18, 19, 20], "middl": 5, "exact": [5, 10, 15, 19], "center": [5, 9, 20], "shift": 5, "respect": [5, 19], "model": [5, 11], "yule": [5, 11], "dichotom": [5, 11], "random": [5, 11, 16, 19, 20], "all": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 20], "necessari": [5, 11, 15, 17, 19], "too": [5, 7, 11, 12, 19], "collect": [5, 8, 11, 16, 19, 20], "letter": [5, 7, 11, 15], "hard": [5, 11], "everi": [5, 9, 11, 15, 16, 19], "step": [5, 11, 17, 19], "randomli": [5, 7, 11], "select": [5, 9, 11, 19], "grow": [5, 11, 19], "uniform": [5, 11], "pda": [5, 11], "interior": [5, 11], "newli": [5, 11], "intern": [5, 7, 9, 10, 11, 15, 17, 19, 20], "child_po": 5, "seri": [5, 9, 11], "dicotomi": [5, 11], "polytomi": [5, 11, 19], "ha": [5, 6, 9, 11, 15, 16, 18, 19], "dicotom": [5, 11], "modif": [5, 11, 20], "arbitrari": [5, 11, 18, 20], "should": [5, 7, 11, 12, 15, 16, 19, 20], "resolv": [5, 11], "otherwis": [5, 10, 11, 15, 16], "do": [5, 11, 12, 15, 16, 18, 19, 20], "still": [5, 11], "Its": [5, 7, 19], "lost": [5, 19], "outgroup": [5, 11, 14], "futur": [5, 11, 17], "put": [5, 9, 11, 16], "kei": [5, 7, 17, 19], "place": [5, 11, 12, 15, 19, 20], "n1": [5, 16, 19, 20], "n2": [5, 16, 19, 20], "swap": 5, "dendrogram": 5, "equidist": [5, 11, 16], "order": [5, 11, 15, 16, 17, 19, 20], "is_leaf_fn": [5, 6, 7, 11, 19], "breadth": [5, 11], "convent": [5, 11, 19], "real": [5, 11, 15, 20], "typic": [5, 11], "just": [5, 11, 15, 18, 19], "hang": [5, 11, 19], "updat": [5, 8, 9, 10, 11, 15, 17], "iter": [5, 7, 8, 11, 18], "except": [6, 18, 19], "newickerror": 6, "content_repr": 6, "dump": [6, 10, 15, 17], "fp": 6, "format_root_nod": [6, 7, 11], "represent": [6, 7, 8, 9, 11, 16, 19, 20], "error": [6, 9, 11, 18], "text": [6, 8, 9, 11, 15, 16, 17, 19, 20], "get_extended_prop": 6, "extract": [6, 9, 17], "nhx": [6, 15, 19], "foo": 6, "bar": [6, 9], "get_prop": [6, 11], "abc": 6, "123": 6, "load": [6, 9, 11, 15, 17, 19, 20], "tree_text": 6, "tree_class": 6, "make_pars": 6, "int": [6, 9, 20], "prop_repr": 6, "accept": [6, 11, 16, 17, 18, 19, 20], "quot": [6, 16, 18], "escaped_char": 6, "n": [6, 8, 9, 11, 15, 16, 18, 19, 20], "charact": [6, 15], "escap": 6, "read_cont": 6, "unicod": 6, "po": [6, 9], "u": [6, 16, 19, 20], "read_nod": 6, "nodes_text": 6, "thei": [6, 7, 11, 15, 16, 17, 19, 20], "repr_short": 6, "obj": 6, "max_len": 6, "limit": [6, 9, 15, 18, 19, 20], "skip_quoted_nam": 6, "skip_spaces_and_com": 6, "after": [6, 7, 11, 15, 16, 19, 20], "whitespac": 6, "comment": [6, 8], "unquot": 6, "nexuserror": 6, "apply_transl": 6, "translat": [6, 7, 10, 15, 17], "get_command": 6, "text_sect": 6, "command": [6, 9, 16, 19], "get_sect": 6, "section_nam": 6, "arg": [6, 9, 20], "section": [6, 16, 19], "full": [6, 11, 15, 16, 19], "get_tre": 6, "transform": 6, "done": [6, 15, 16, 19], "alg_format": [7, 15], "fasta": [7, 8, 15, 16], "sp_naming_funct": [7, 15, 17], "store": [7, 8, 9, 11, 12, 15, 16, 17, 19], "extend": [7, 9, 11, 15, 19], "standard": [7, 11, 19, 20], "ad": [7, 10, 11, 14, 16, 17, 19, 20], "specif": [7, 16, 17, 19, 20], "phylogent": 7, "initi": [7, 9, 15, 16, 20], "which": [7, 11, 15, 16, 17, 19, 20], "contain": [7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "phylip": [7, 8], "iphylip": [7, 8, 15], "interleav": [7, 8], "get": [7, 9, 10, 14, 15, 16, 18], "set_species_naming_funct": [7, 15], "identifi": [7, 9, 15, 17], "annotate_gtdb_taxa": [7, 17], "taxid_attr": [7, 10, 17], "tax2nam": [7, 10, 17], "tax2track": [7, 10, 17], "tax2rank": [7, 10, 17], "dbfile": [7, 10], "annotate_ncbi_taxa": [7, 17], "ncbi": [7, 10, 14], "encod": [7, 8, 11, 15, 19], "taxid": [7, 9, 10, 14], "spname": 7, "scientif": [7, 9, 10, 17, 20], "spci": 7, "named_lineag": [7, 10, 17], "track": [7, 10, 17], "inform": [7, 9, 11, 14, 16, 19, 20], "access": [7, 15, 16, 17, 19, 20], "dictionari": [7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "avoid": [7, 8, 16, 19], "queri": [7, 16, 17, 19], "rank": [7, 10, 17], "param": 7, "local": [7, 10, 14, 16, 18], "copi": [7, 11, 14, 20], "tax2lineag": [7, 17], "collapse_lineage_specific_expans": [7, 15], "return_copi": 7, "expans": [7, 15], "tip": [7, 9, 11, 18, 19], "chosen": 7, "within": [7, 9, 11, 14, 15, 16, 17], "suppli": [7, 11], "criteria": [7, 11], "prune": [7, 9, 10, 11, 14, 15, 16, 17], "process": [7, 9, 15, 17, 19], "get_ag": [7, 15], "species2ag": [7, 15], "phylostratigraf": 7, "describ": [7, 11, 15, 16, 18], "gabaldon": [7, 15], "2011": [7, 15], "assign": [7, 9, 11, 15, 17], "event": [7, 9, 14], "rel": [7, 11, 14, 18], "tempor": [7, 15], "scale": [7, 9, 15, 16], "wide": [7, 15, 19], "studi": [7, 15], "27": [7, 16], "38": 7, "45": [7, 16, 17, 20], "get_age_balanced_outgroup": 7, "better": [7, 19], "balanc": [7, 11, 19], "ag": [7, 15], "get_descendant_evol_ev": [7, 15], "sos_thr": [7, 15], "speciat": [7, 15, 19], "overlap": [7, 16, 19], "linag": [7, 17], "detail": [7, 19, 20], "human": [7, 9, 11, 15, 19, 20], "phylom": 7, "dopazo": 7, "2007": [7, 15], "r109": 7, "get_farthest_oldest_leaf": [7, 15], "oldest": [7, 15], "requir": [7, 10, 11, 15, 17, 18, 19, 20], "estim": [7, 20], "pointer": [7, 19, 20], "receiv": [7, 11, 20], "uniqu": [7, 9, 11, 17], "dynam": [7, 11, 15, 16, 19, 20], "collaps": [7, 9, 10, 11], "get_farthest_oldest_nod": [7, 15], "seq": [7, 8, 16, 20], "get_my_evol_ev": [7, 15], "involv": [7, 15, 19], "scan": [7, 15], "dup": [7, 15], "algorithm": [7, 16, 19], "leafnam": 7, "get_speciation_tre": [7, 15], "map_properti": 7, "autodetect_dupl": [7, 15], "newick_onli": [7, 15], "possibl": [7, 9, 11, 15, 19, 20], "gene": [7, 9, 11, 14], "famili": [7, 11, 14, 17, 20], "marcet": [7, 15], "map": [7, 11, 15, 16], "subtre": [7, 9, 12, 16, 18, 19, 20], "get_descendants_evol_ev": 7, "evoltyp": [7, 15], "get_speci": [7, 15], "cover": 7, "iter_speci": 7, "link_to_align": [7, 15], "kwarg": [7, 8, 9], "ncbi_compar": 7, "cached_cont": [7, 11], "reconcil": [7, 15], "species_tre": 7, "reconcili": 7, "evolutionari": [7, 9, 14, 19], "infer": [7, 15, 17, 19], "take": [7, 15, 17, 18, 19], "nodenam": 7, "parse_sp_nam": 7, "node_nam": 7, "split": [7, 17, 19], "_": [7, 15, 19], "split_by_dup": [7, 15], "outfil": [7, 8, 11, 19], "str": [7, 9, 11], "output": [7, 8, 11, 15, 16, 18], "instad": [7, 11], "avail": [7, 9, 11, 15, 16, 19, 20], "bool": [7, 9, 11], "compat": [7, 11, 19], "reason": [7, 11, 15, 18, 19], "sci_nam": [7, 9, 10, 11, 17], "ocur": 7, "etyp": [7, 15], "l": [7, 15, 19, 20], "loss": [7, 15], "in_seq": [7, 15], "side": [7, 11, 16], "out_seq": [7, 15], "sequenci": 8, "fix_dupl": 8, "path": [8, 11, 15, 19, 20], "altern": [8, 10, 15, 19], "forc": 8, "To": [8, 11, 15, 16, 17, 19, 20], "effect": [8, 11], "relax": 8, "phylip_relax": 8, "iphylip_relax": 8, "seqs_str": 8, "seq1": 8, "aaaaaaaaaaa": 8, "seq2": 8, "ttttttttttttt": 8, "get_seq": [8, 9, 16], "get_entri": 8, "entri": 8, "iter_entri": 8, "item": [8, 9, 10, 11, 17, 19, 20], "tupl": [8, 9, 11, 20], "set_seq": 8, "written": [8, 20], "keep": [9, 10, 11, 15, 16, 19, 20], "rest": [9, 19, 20], "talk": 9, "world": 9, "id": [9, 11, 16, 19], "delet": [9, 11], "globalstuff": 9, "treedata": 9, "core": [9, 11, 15], "include_prop": [9, 11, 16], "exclude_prop": [9, 11, 16], "timer": 9, "float": [9, 11, 16, 20], "activ": [9, 16], "namedtupl": 9, "0x7f98a5d42a20": 9, "activate_clad": 9, "tree_id": 9, "activate_nod": 9, "add_tre": 9, "add_trees_from_request": 9, "app": 9, "callback": 9, "change_selection_nam": 9, "tid": 9, "copy_styl": 9, "deactivate_clad": 9, "deactivate_nod": 9, "del_tre": 9, "everywher": 9, "appear": [9, 11, 15, 16, 19], "referenc": 9, "find_nod": 9, "get_active_clad": 9, "get_command_search": 9, "appropri": [9, 12, 15], "get_draw": 9, "get_eval_search": 9, "express": [9, 12, 14], "evalu": [9, 16, 18], "get_layout": 9, "get_layouts_from_gett": 9, "layout1": 9, "submodul": 9, "get_newick": 9, "max_mb": 9, "get_next_available_port": 9, "host": [9, 11], "localhost": [9, 11, 16], "port_min": 9, "5000": [9, 11, 16], "port_max": 9, "6000": 9, "next": [9, 11, 19, 20], "port": [9, 11], "socket": 9, "get_nodes_info": 9, "get_par": 9, "count_leav": 9, "get_pars": 9, "get_search_funct": 9, "get_selection_info": 9, "tree_data": 9, "info": [9, 11, 20], "get_select": 9, "get_stat": 9, "pname": 9, "some": [9, 15, 16, 17, 19, 20], "statist": 9, "get_tid": 9, "get_topological_search": 9, "pattern": [9, 12, 18, 19], "get_trees_from_fil": 9, "fileobject": 9, "get_trees_from_form": 9, "form": [9, 11, 16], "request": [9, 11], "get_trees_from_nexus_or_newick": 9, "btext": 9, "name_newick": 9, "safe_mod": 9, "compress": [9, 11], "global": 9, "initialize_tree_styl": 9, "json_error": 9, "load_tre": 9, "load_tree_from_newick": 9, "memori": [9, 10, 19], "mainten": 9, "check_interv": 9, "60": [9, 16, 20], "max_tim": 9, "1800": 9, "perform": [9, 15, 16, 19, 20], "task": [9, 19], "second": [9, 15, 18, 19], "like": [9, 11, 16, 17, 18, 19], "nice_html": 9, "titl": [9, 16], "open_browser_window": 9, "try": [9, 18], "browser": [9, 16], "window": 9, "prune_by_select": 9, "remove_act": 9, "idx": 9, "remove_active_clad": 9, "remove_search": 9, "remove_select": 9, "req_json": 9, "what": [9, 12, 16, 18, 19], "json": 9, "would": [9, 15, 18, 19], "gracefulli": 9, "abort": 9, "retrieve_layout": 9, "retrieve_tree_data": 9, "retriev": [9, 15, 17, 19], "previous": [9, 15, 19, 20], "pickl": [9, 19], "tmp": 9, "run_smartview": 9, "quiet": [9, 11, 16], "keep_serv": [9, 11, 16], "open_brows": [9, 11], "safer": [9, 12], "eval": [9, 12, 16], "search_to_select": 9, "key_text": 9, "sub": [9, 10, 18, 19], "store_act": 9, "store_search": 9, "store_select": 9, "touch_and_get": 9, "unselect_nod": 9, "update_app_available_layout": 9, "update_layout": 9, "active_layout": 9, "front": [9, 11], "statu": 9, "update_node_prop": 9, "update_node_styl": 9, "update_select": 9, "alia": 9, "field": [9, 16], "viewport": 9, "panel": 9, "zoom": [9, 16], "collapsed_id": [9, 16], "subclass": 9, "extra": [9, 16, 18, 19, 20], "collapse_s": [9, 16], "min_siz": [9, 16], "npanel": 9, "draw_aligned_head": 9, "draw_collaps": 9, "collapsed_nod": 9, "active_children": 9, "selected_children": 9, "draw_cont": 9, "draw_nod": 9, "bdx": 9, "bdy": 9, "bdy0": 9, "bdy1": 9, "flush_outlin": 9, "minimum_dx": 9, "box": [9, 16], "outlin": 9, "reset": 9, "get_active_children": 9, "get_collapsed_nod": 9, "either": [9, 17, 19], "get_outlin": 9, "get_popup_prop": 9, "safe": [9, 19], "popup": [9, 11], "get_selected_children": 9, "is_fully_collaps": 9, "utterli": 9, "width": [9, 11, 16, 20], "on_first_visit": 9, "on_last_visit": 9, "draweraligncircfac": 9, "draweralignrectfac": 9, "drawercirc": 9, "minim": [9, 10], "circular": [9, 16, 19], "circ": 9, "content_s": 9, "draw_childrenlin": 9, "p1": 9, "p2": 9, "arc": 9, "span": 9, "draw_lengthlin": 9, "parent_of": 9, "line": [9, 11, 16, 19, 20], "draw_nodebox": 9, "searched_bi": 9, "draw_nodedot": 9, "max_siz": 9, "active_nod": 9, "minimum_dr": 9, "get_box": 9, "in_viewport": 9, "is_smal": 9, "node_s": 9, "drawercircfac": 9, "bdr": 9, "bda": 9, "bda0": 9, "bda1": 9, "drawerrect": 9, "rectangular": [9, 16, 20], "rect": [9, 20], "circl": [9, 16, 20], "squar": [9, 16], "sm_style": [9, 11, 16], "drawerrectfac": 9, "dx": [9, 16], "dy": [9, 16], "treeactiv": 9, "clade": [9, 17], "drawn_siz": 9, "min_x": 9, "get_asec": 9, "annular": 9, "sector": 9, "get_empty_act": 9, "get_rect": 9, "rectangl": [9, 16], "make_box": 9, "safe_str": 9, "stack": 9, "box1": 9, "box2": 9, "pad": [9, 11, 16], "cartesian": 9, "circumasec": 9, "circumscrib": 9, "circumrect": 9, "asec": 9, "clip_angl": 9, "a1": [9, 16, 20], "a2": [9, 16, 20], "angl": 9, "pi": 9, "draw_arc": 9, "larg": [9, 11, 16, 19], "arc_typ": 9, "draw_arrai": 9, "tooltip": [9, 16], "draw_arrow": 9, "orient": 9, "arrow_typ": 9, "arrow": 9, "bound": 9, "draw_circl": 9, "radiu": [9, 20], "circle_typ": 9, "draw_ellips": 9, "rx": 9, "ry": 9, "ellipse_typ": 9, "draw_html": 9, "html_type": 9, "draw_img": 9, "img": 9, "img_typ": 9, "draw_lin": 9, "line_typ": 9, "draw_outlin": 9, "draw_rect": 9, "rect_typ": 9, "draw_rhombu": 9, "rhombus_typ": 9, "rhombu": 9, "draw_slic": 9, "da": 9, "slice_typ": 9, "draw_text": [9, 16], "text_typ": 9, "rotat": [9, 16], "anchor": 9, "draw_triangl": 9, "triangle_typ": 9, "triangl": [9, 16], "defin": [9, 15, 17, 18, 19, 20], "top": [9, 11, 16, 19, 20], "left": [9, 16, 19], "first_valu": 9, "get_line_typ": 9, "get_x": 9, "get_i": 9, "intersects_angl": 9, "part": [9, 15, 17, 18, 19, 20], "intersects_box": 9, "b1": [9, 16, 20], "b2": [9, 16, 20], "kind": [9, 18, 19], "intersect": 9, "intersects_seg": 9, "s1": 9, "s2": 9, "segment": 9, "split_thru_negative_xaxi": 9, "cut": [9, 11, 19], "summari": 9, "summar": 9, "alignlinkfac": 9, "stroke_color": 9, "grai": [9, 16, 20], "stroke_width": 9, "opac": [9, 16, 20], "solid": [9, 16, 20], "dot": [9, 11, 16, 20], "dash": [9, 16, 20], "compute_bounding_box": 9, "dx_to_closest_child": 9, "n_row": 9, "n_col": 9, "dx_befor": 9, "dy_befor": 9, "fit": 9, "overriden": 9, "inherit": [9, 16], "alignmentfac": [9, 16], "seqtyp": [9, 16], "aa": [9, 16, 19], "gap_format": [9, 16, 20], "seq_format": [9, 16, 20], "height": [9, 11, 16, 19, 20], "fgcolor": [9, 16, 20], "black": [9, 16, 19, 20], "bgcolor": [9, 16, 20], "bcc3d0": [9, 16], "gapcolor": [9, 16, 20], "gap_linewidth": [9, 16], "max_fsiz": [9, 16], "12": [9, 16, 17, 19, 20], "ftype": [9, 16], "san": [9, 16], "serif": [9, 16], "padding_x": [9, 16], "padding_i": [9, 16], "build_block": 9, "arrowfac": 9, "color": [9, 19, 20], "5px": 9, "min_fsiz": [9, 16], "15": [9, 11, 16, 19, 20], "attr": 9, "formatt": [9, 16], "get_cont": 9, "circlefac": [9, 16, 20], "et": [9, 10, 11, 14, 15, 16, 17, 18, 20], "piec": [9, 16, 20], "compute_fs": 9, "zx": [9, 16], "zy": [9, 16], "in_aligned_viewport": 9, "htmlface": 9, "imgfac": [9, 20], "img_path": [9, 20], "legendfac": 9, "colormap": [9, 16], "outlinefac": 9, "collapsing_height": 9, "piechartfac": 9, "compute_pi": 9, "rectfac": [9, 16], "scalefac": [9, 16], "scale_rang": [9, 16], "tick_width": [9, 16], "80": [9, 16], "line_width": [9, 16], "0f": [9, 16], "selectedcirclefac": 9, "selectedfac": 9, "selectedrectfac": 9, "seqfac": [9, 16, 20], "poswidth": [9, 16], "seqmotiffac": [9, 16, 20], "motif": [9, 16, 20], "build_region": 9, "region": 9, "stackedbarfac": 9, "whatev": 9, "textfac": [9, 16, 20], "alignedgrid": 9, "facecontain": 9, "grid": 9, "horizont": [9, 16], "idea": [9, 11, 18, 19], "header": [9, 11, 16], "footer": [9, 16], "col": [9, 20], "face1": 9, "face2": 9, "add_fac": [9, 11, 16, 20], "make_fac": 9, "karg": [9, 20], "attribut": [9, 10, 11, 14, 15, 16, 17, 20], "node_style_default": 9, "draw_descend": [9, 16], "mark": 9, "hz_line_width": [9, 16, 20], "pixel": [9, 11, 16, 20], "normal": [9, 15, 17, 18, 19, 20], "vt_line_width": [9, 16, 20], "vertic": [9, 16], "init": 9, "aligned_fac": [9, 16], "legend": 9, "set_node_styl": [9, 16], "set_tree_styl": [9, 16], "cased_nam": 9, "txt": 9, "active_fac": 9, "active_face_po": 9, "add_legend": [9, 16], "variabl": [9, 14, 16], "discret": [9, 16], "value_rang": [9, 16], "color_rang": [9, 16], "aligned_panel_foot": [9, 16], "aligned_panel_head": [9, 16], "get_legend": 9, "selected_fac": 9, "selected_face_po": 9, "layoutgenomiccontext": 9, "nside": 9, "conservation_threshold": 9, "70": [9, 16, 20], "gene_nam": 9, "tooltip_prop": 9, "anchor_stroke_color": 9, "anchor_stroke_width": 9, "3px": 9, "non_conserved_color": 9, "d0d0d0": 9, "collapse_conserv": 9, "collapse_by_conserv": 9, "get_context": 9, "get_tooltip": 9, "layoutbranchlength": 9, "branch_top": [9, 11, 16], "8d8d8d": 9, "layoutbranchsupport": 9, "branch_bottom": [9, 11, 16], "fa8072": 9, "layoutleafnam": 9, "branch_right": [9, 11, 16], "layoutnumberleav": 9, "collapsed_onli": [9, 11, 16], "layoutoutlin": 9, "lightgrai": 9, "layoutpfamdomain": 9, "pfam": 9, "layoutsmartdomain": 9, "smart": [9, 16], "21": 9, "layoutbestnam": 9, "best_nam": 9, "best": [9, 10, 15, 18, 20], "layoutbigg": 9, "bigg": 9, "layoutcard": 9, "card": 9, "layoutcazi": 9, "cazi": 9, "layoutevolev": 9, "speciation_color": 9, "blue": [9, 16, 20], "duplication_color": 9, "red": [9, 16, 20], "layoutkeggenzym": 9, "kegg_enzym": 9, "kegg": 9, "enzym": 9, "layoutkeggmodul": 9, "kegg_modul": 9, "11": [9, 15, 16, 19], "layoutkeggnumb": 9, "kegg_numb": 9, "layoutkeggpathwai": 9, "kegg_pathwai": 9, "pathwai": 9, "layoutlastcommonancestor": 9, "rect_width": 9, "1000": [9, 11, 16], "shown": [9, 15, 16, 20], "get_color": 9, "layoutpdb": 9, "pdb": 9, "layoutproteinnam": 9, "prot_nam": 9, "layoutscientificnam": 9, "layoutetediffdist": 9, "diff": 9, "diff_node_color": 9, "a50000": 9, "diff_node_s": 9, "layouthumanog": 9, "og": 9, "human_orth_prop": 9, "human_orth": 9, "6b92d6": 9, "layoutucsc": 9, "ucsc": 9, "nodecolor": 9, "800000": 9, "nodes": 9, "textcolor": 9, "c43b5d": 9, "layoutucsctran": 9, "tran": 9, "ucsc_trans_prop": 9, "ucsc_tran": 9, "get_layout_evoltyp": 9, "get_layout_gnam": 9, "get_layout_lca_rect": 9, "get_layout_ogs_egg5": 9, "get_layout_scinam": 9, "layoutalign": 9, "700": 9, "rang": [9, 15, 16, 20], "summarize_inner_nod": 9, "layoutautonam": 9, "auto": 9, "text_color": 9, "grei": 9, "layoutcuratednam": 9, "layouteukog": 9, "euk": 9, "layoutpreferrednam": 9, "fb3640": 9, "layoutscinam": 9, "layoutse": 9, "seed": [9, 11], "layoutbarplot": 9, "200": [9, 16, 20], "size_prop": 9, "color_prop": 9, "color_gradi": [9, 16], "taxdump_fil": 10, "transpar": [10, 16, 17, 20], "connector": 10, "connect": [10, 11, 17, 19], "system": [10, 20], "download": [10, 15, 17], "site": 10, "annotate_tre": 10, "deriv": [10, 20], "get_broken_branch": 10, "taxa_lineag": 10, "n2content": 10, "monophylet": [10, 11, 19], "well": [10, 15, 19], "affect": [10, 15, 19, 20], "experiment": 10, "get_common_nam": 10, "get_descendant_taxa": [10, 17], "intermediate_nod": [10, 17], "rank_limit": 10, "collapse_subspeci": [10, 17], "return_tre": [10, 17], "get_fuzzy_name_transl": 10, "sim": 10, "score": [10, 15, 19], "taxa": [10, 14], "similar": [10, 12, 16, 17, 19], "min": 10, "report": [10, 17], "get_lineag": [10, 17], "hierarch": [10, 11, 19, 20], "get_lineage_transl": 10, "get_name_transl": [10, 17], "get_rank": [10, 17], "get_taxid_transl": [10, 17], "try_synonym": 10, "get_topologi": [10, 17], "complet": [10, 15, 16, 19, 20], "kept": [10, 11, 16, 17, 19, 20], "rid": 10, "strain": 10, "upper": [10, 19], "translate_to_nam": [10, 17], "update_taxonomy_databas": [10, 17], "latest": [10, 17], "taxdump": [10, 17], "tar": [10, 17], "gz": [10, 17], "locat": [10, 19, 20], "tax": 10, "gtdb": [10, 14], "get_name_lineag": 10, "taxnam": 10, "anoth": [10, 11, 16, 19], "gtdbtaxdump": 10, "consist": [11, 16, 17, 19], "hampshir": [11, 19], "add_child": [11, 19], "supli": 11, "add_children": 11, "add_face_smartview": 11, "fix": [11, 15], "alwai": [11, 15, 18, 19], "attach": [11, 15, 16, 20], "independ": [11, 16, 19, 20], "go": [11, 18, 19], "posibl": 11, "add_face_treeview": 11, "integ": 11, "bottom": [11, 16, 20], "behind": 11, "add_featur": 11, "pr_name": 11, "pr_valu": 11, "add_prop": [11, 16, 17, 19, 20], "add_sist": [11, 19], "include_root": 11, "up": [11, 14, 18, 19, 20], "check_monophyli": [11, 19], "is_monophylet": 11, "clade_typ": 11, "leaves_extra": 11, "being": [11, 15, 19], "monophyli": [11, 14], "collapsed_fac": 11, "ref_tre": 11, "use_collater": 11, "min_support_sourc": 11, "min_support_ref": 11, "has_dupl": 11, "expand_polytomi": 11, "max_treeko_splits_to_be_artifact": 11, "ref_tree_attr": 11, "source_tree_attr": 11, "robinson": 11, "fould": 11, "symmetr": 11, "share": [11, 17, 19], "edg": [11, 16, 19], "cophenetic_matrix": 11, "cophenet": 11, "matrix": 11, "z": 11, "gist": 11, "github": [11, 16, 17], "279f9009f46bf675e3a890c19191158b": 11, "orderless": 11, "Then": 11, "xor": 11, "both": [11, 15, 16, 19, 20], "those": [11, 15, 16], "One": [11, 16, 18, 19, 20], "optim": 11, "sinc": [11, 15, 17, 18, 19], "itself": [11, 19], "zero": [11, 19], "itertool": 11, "combin": [11, 14, 15, 17], "rather": [11, 15, 17], "permut": [11, 18], "our": [11, 15, 16, 18, 19, 20], "theta": 11, "2n": 11, "o": [11, 16, 19, 20], "great": 11, "realiti": 11, "speed": [11, 15], "thing": [11, 18], "dimension": 11, "cpickl": [11, 19], "protocol": 11, "serialis": [11, 19], "thu": [11, 15, 16, 19, 20], "exclud": [11, 19], "As": [11, 15, 16, 19], "whole": [11, 15, 17, 19, 20], "clone": [11, 19], "slower": [11, 19], "recommend": [11, 19], "deepcopi": [11, 19], "slowest": [11, 19], "complex": [11, 16, 18, 19], "even": [11, 15, 16, 17, 19, 20], "etc": [11, 16, 18, 20], "del_featur": 11, "perman": 11, "del_prop": [11, 19], "prop_nam": [11, 19], "prevent_nondicotom": 11, "preserve_branch_length": [11, 19], "transfer": [11, 19], "until": 11, "occur": 11, "among": [11, 15, 16, 19], "to_str": [11, 15, 17, 18, 19], "levelord": [11, 12, 19], "detach": 11, "conserv": 11, "mechan": 11, "past": [11, 19], "pair": [11, 15, 16, 20], "lai": 11, "pass": [11, 15, 16, 17, 18, 19, 20], "won": 11, "recomput": 11, "map_prop": 11, "polytomy_size_limit": 11, "skip_large_polytomi": 11, "solut": [11, 19], "multifurc": [11, 14], "pleas": 11, "binari": 11, "exponenti": 11, "feasibl": 11, "105": [11, 16, 20], "945": 11, "10395": 11, "135135": 11, "2027025": 11, "ajmonlin": 11, "2010": 11, "darwin": 11, "php": 11, "show_branch_length": [11, 16, 20], "show_branch_support": [11, 16, 20], "launch": 11, "interact": [11, 14], "session": [11, 18, 20], "__name__": [11, 20], "adress": 11, "listen": [11, 16], "static": [11, 16, 20], "from_parent_child_t": 11, "parent_child_t": 11, "tabl": [11, 16, 20], "relationship": [11, 15, 19], "from_skbio": 11, "skbio_tre": 11, "map_attribut": 11, "scikit": 11, "bio": 11, "treenod": 11, "from_skibio": 11, "skbiotre": 11, "get_cached_cont": [11, 18, 19], "container_typ": 11, "leaves_onli": 11, "serv": [11, 17], "cach": [11, 14, 18], "And": [11, 15, 19, 20], "themselv": [11, 19], "get_children": 11, "get_closest_leaf": 11, "closest": 11, "get_dist": [11, 19], "target": [11, 16, 19], "target2": 11, "get_farthest_leaf": [11, 19], "get_farthest_nod": [11, 19], "get_midpoint_outgroup": [11, 19], "divid": 11, "get_monophylet": [11, 19], "consid": [11, 15, 19], "exclus": [11, 19], "get_sist": 11, "get_topology_id": 11, "bunch": 11, "without": [11, 15, 19], "sure": 11, "befor": [11, 16, 18, 19, 20], "hop": 11, "img_styl": [11, 20], "_get_styl": 11, "init_from_et": 11, "init_from_newick": 11, "is_collaps": 11, "_get_collaps": 11, "is_initi": 11, "_get_initi": 11, "is_root": [11, 16, 18, 19], "iter_prepostord": 11, "postord": [11, 19], "flag": [11, 15, 19], "visit": [11, 19], "leaf_nam": [11, 20], "pop_child": 11, "child_idx": 11, "uniformli": 11, "42": 11, "retain": 11, "minimum": 11, "k": [11, 18, 19], "remove_child": [11, 19], "exit": 11, "longer": [11, 20], "remove_children": 11, "remove_sist": 11, "file_nam": 11, "px": [11, 20], "dpi": [11, 20], "90": [11, 16, 20], "imag": [11, 14, 16], "svg": [11, 16, 20], "pdf": [11, 16, 20], "png": [11, 20], "mm": [11, 15, 20], "millimet": [11, 20], "inch": [11, 20], "resolut": [11, 20], "per": [11, 15, 20], "reverse_children": 11, "robinson_fould": [11, 19], "prop_t1": 11, "prop_t2": 11, "unrooted_tre": [11, 19], "correct_by_polytomy_s": 11, "min_support_t1": 11, "min_support_t2": 11, "rf": [11, 19], "rf_max": [11, 19], "edges_t1": 11, "edges_t2": 11, "discarded_edges_t1": 11, "discarded_edges_t2": 11, "expand": [11, 19], "absolut": [11, 15], "search_ancestor": [11, 19], "condit": [11, 12, 16, 18, 19], "search_descend": [11, 19], "search_leaves_by_nam": [11, 19], "search_nod": [11, 15, 19], "set_styl": [11, 16, 20], "node_styl": [11, 20], "doubl": 11, "_get_sm_styl": 11, "sort_descend": 11, "delete_orphan": 11, "swap_children": 11, "show_intern": [11, 15, 19], "compact": [11, 18, 19], "py": [11, 16, 20], "px0": 11, "cascad": 11, "ascii": 11, "exactli": 11, "overrid": 11, "three": [11, 15, 16, 18, 19], "bf": 11, "depth": [11, 19], "df": 11, "preorder": [11, 19], "someth": [12, 18], "re": [12, 18, 19, 20], "satisfi": [12, 16], "constraint": 12, "strongli": [12, 19], "restrict": 12, "keyword": 12, "constructor": [12, 19, 20], "context": [12, 16, 18], "understand": [14, 16], "faster": [14, 15], "lookup": 14, "concaten": 14, "solv": 14, "overview": 14, "taxonom": [14, 17], "date": 14, "aspect": 14, "less": [14, 19], "outsid": 14, "suit": [14, 16], "most": [15, 16, 17, 18, 19], "molecular": [15, 16, 20], "homolog": 15, "deal": [15, 19], "while": [15, 17, 20], "ancestr": 15, "direct": 15, "consequ": 15, "msa": [15, 16], "document": [15, 16, 20], "applic": 15, "unalign": 15, "mai": [15, 19], "fasta_txt": 15, "seqa": 15, "maeipdetiqqfmalt": 15, "hniavqylsefgtddikdrreeah": 15, "seqb": 15, "maeipdatiqqfmaltnvshniavqi": 15, "efgtddqkdrreeah": 15, "seqc": 15, "maeipdatiq": 15, "altnvshniavqylsefgtddqpdrreeah": 15, "seqd": 15, "maeapdetiqqfmaltnvshniavqylsefg": 15, "reeah": 15, "time": [15, 17, 18, 19, 20], "strict": [15, 19], "perfect": 15, "onc": [15, 16, 17, 19, 20], "through": [15, 16, 17, 19, 20], "hniavqylsefgdlnealnsyyasqtddikdrreeah": 15, "efgdlnealnsyyayqtddqkdrreeah": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeah": 15, "maeapdetiqqfmaltnvshniavqylsefgdln": 15, "iphylip_txt": 15, "76": 15, "maeipdetiq": 15, "qfmalt": 15, "niavqylsef": 15, "gdlnealnsi": 15, "yasqtddikd": 15, "rreeahqfma": 15, "qfmaltnvsh": 15, "niavqi": 15, "ef": [15, 19], "yayqtddqkd": 15, "altnvsh": 15, "yasqtddqpd": 15, "maeapdetiq": 15, "gdlneal": 15, "reeahq": 15, "ltnvshqfma": 15, "ltnvsh": 15, "fma": 15, "usual": [15, 17, 19], "now": [15, 16, 18, 19, 20], "let": [15, 16, 18, 19, 20], "fmaltnvsh": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqfmaltnvshqfmaltnvsh": 15, "efgdlnealnsyyayqtddqkdrreeahqfmaltnvsh": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqf": 15, "maltnvshqfmaltnvsh": 15, "efgdlnealnsi": 15, "yayqtddqkdrreeahqfmaltnvsh": 15, "altnvshnia": 15, "vqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "maeapd": 15, "etiqqfmaltnvshniavqylsefgdln": 15, "reload": 15, "sametre": 15, "recov": 15, "benefit": 15, "programm": [15, 16, 20], "built": [15, 16, 19, 20], "conveni": [15, 17, 19], "alg": 15, "dme_001": 15, "hniavqylsefgdln": 15, "yyasqtddikdrreeah": 15, "dme_002": 15, "cfa_001": 15, "mms_001": 15, "hsa_001": 15, "ptr_002": 15, "fmaltnvshniavqi": 15, "yqtddqkdrreeah": 15, "mmu_002": 15, "hsa_002": 15, "maeapdetiqqfm": 15, "ltnvshniavqylsefgdln": 15, "mmu_001": 15, "ptr_001": 15, "gene_tree_nw": 15, "species_tree_nw": 15, "hsa": [15, 20], "ptr": [15, 20], "mmu": 15, "cfa": [15, 20], "dme": [15, 20], "genetre": 15, "sptree": 15, "recon_tre": 15, "separ": [15, 19], "obtain": [15, 19], "often": [15, 18, 19], "establish": [15, 19], "behavior": 15, "get_species_nam": 15, "node_name_str": 15, "underscor": 15, "spcode": [15, 17], "code2nam": [15, 20], "drosophila": [15, 20], "melanogast": [15, 20], "homo": [15, 16, 17, 20], "sapien": [15, 17, 20], "troglodyt": [15, 17, 20], "mu": [15, 17, 20], "musculu": [15, 17, 20], "cani": [15, 20], "familiari": [15, 20], "disabl": [15, 19], "overwriten": 15, "mynewick": 15, "chimp": [15, 20], "dog": [15, 20], "mous": [15, 16, 20], "fly": [15, 16, 20], "charleston": 15, "1997": 15, "paralogi": 15, "houben": 15, "2009": 15, "appli": [15, 16, 17, 19, 20], "threshold": [15, 16], "rise": 15, "adjust": [15, 16, 20], "human_seq": 15, "ev": 15, "join": 15, "interest": [15, 19], "filter": [15, 19], "fseq": 15, "slist": 15, "startswith": [15, 16, 20], "besid": 15, "predict": 15, "labl": 15, "predefin": [15, 20], "explain": 15, "strictli": [15, 19], "taxonomic_info": 15, "fir": 15, "inparalog": 15, "ortholog": 15, "elif": [15, 16, 20], "outparalog": 15, "notic": 15, "state": 15, "addition": [15, 19], "phylo": 15, "paralog": 15, "similarli": [15, 19], "therefor": [15, 16, 19], "certain": [15, 19], "although": [15, 16, 19, 20], "precis": 15, "approach": [15, 17, 19], "synonym": 15, "rate": 15, "proxi": 15, "diverg": 15, "al": 15, "kalinka": 15, "2001": 15, "aim": 15, "gradient": 15, "primat": [15, 17, 19, 20], "mammal": [15, 20], "vertebr": 15, "abov": [15, 16, 17, 19, 20], "categori": 15, "orangutan": 15, "fish": [15, 20], "relative_dist": 15, "non": 15, "rat": 15, "purpos": 15, "humana": 15, "chimpa": 15, "dup1": 15, "humanb": 15, "chimpb": 15, "mousea": 15, "dup3": 15, "humanc": 15, "chimpc": 15, "dup2": 15, "humand": 15, "ratc": 15, "mousec": 15, "distant": [15, 19], "lett": 15, "hsa_003": 15, "hsa_004": 15, "ptr_004": 15, "mmu_004": 15, "older": 15, "belong": [15, 20], "hominid": 15, "macaca": 15, "mulata": 15, "metazoa": [15, 17, 19], "correspondig": 15, "age2nam": 15, "event1": 15, "event2": 15, "lead": 15, "vari": 15, "assist": [15, 19], "autodetect": 15, "miss": [15, 19], "useless": 15, "observ": 15, "subpart": [15, 19], "becaus": [15, 16], "combinatori": 15, "background": 15, "enorm": 15, "few": [15, 18], "hundr": 15, "ten": 15, "thousand": 15, "here": [15, 16, 17, 19, 20], "human_1": 15, "chimp_1": 15, "human_2": 15, "chimp_2": 15, "chimp_3": 15, "fish_1": 15, "human_3": 15, "fish_3": 15, "yeast_2": 15, "yeast_1": 15, "yeast": [15, 19], "ignor": [15, 17], "ntree": 15, "ndup": 15, "spt": 15, "map_featur": 15, "effici": [15, 17, 18], "significantli": 15, "much": 15, "simpler": 15, "previou": [15, 16, 18, 19], "easili": [15, 17, 19, 20], "novel": 16, "enhanc": 16, "introduc": [16, 17], "v4": [16, 17], "essenti": [16, 17, 19], "foundat": 16, "v3": 16, "fundament": 16, "compon": 16, "highli": [16, 20], "adapt": [16, 17], "backbon": 16, "variou": 16, "choos": [16, 20], "treelayout": 16, "graph": [16, 19, 20], "geometr": [16, 20], "shape": [16, 20], "sequencefac": [16, 20], "These": [16, 17, 19], "upgrad": 16, "entir": [16, 19], "individu": 16, "act": [16, 20], "hook": [16, 20], "framework": 16, "drawn": [16, 20], "drawer": 16, "henc": 16, "understood": [16, 19, 20], "rule": [16, 20], "scheme": [16, 19], "fulli": [16, 17, 20], "integr": [16, 17, 20], "interfac": [16, 20], "gui": [16, 19, 20], "simpli": [16, 20], "advantag": [16, 20], "interrupt": [16, 20], "continu": [16, 20], "execut": [16, 20], "made": [16, 20], "quit": [16, 18, 20], "special": [16, 18, 19, 20], "dure": [16, 20], "util": [16, 17], "environ": 16, "ipython": 16, "jupyt": 16, "notebook": 16, "below": [16, 19, 20], "demonstr": 16, "usag": 16, "explore_standalon": 16, "sep": 16, "16": [16, 20], "2021": 16, "13": [16, 19], "09": [16, 19], "58": 16, "copyright": 16, "credit": 16, "licens": 16, "29": 16, "help": [16, 17], "action": [16, 19], "bottl": 16, "v0": 16, "25": [16, 20], "wsgirefserv": 16, "hit": 16, "ctrl": 16, "127": 16, "02": 16, "nov": 16, "2023": 16, "19": 16, "303": 16, "106": 16, "30": [16, 20], "nodecount": 16, "all_select": 16, "all_act": 16, "555": 16, "284": 16, "40000000000003": 16, "za": 16, "33333333333333337": 16, "16666666666666666": 16, "3333333333333335": 16, "333333333333333": 16, "5b": 16, "5d": 16, "22default": 16, "3abranch": 16, "22": 16, "2c": 16, "3aleaf": 16, "1765": 16, "explore_show": 16, "click": 16, "decid": [16, 19], "Or": [16, 17, 19, 20], "trig": 16, "targer": 16, "major": 16, "smaller": [16, 19], "whether": 16, "deactiv": 16, "minimap": 16, "hover": 16, "cursor": 16, "tend": 16, "occupi": 16, "area": [16, 20], "button": 16, "input": [16, 17, 19], "histori": 16, "modtifi": 16, "insensit": 16, "lower": [16, 19], "sensit": 16, "prefix": 16, "regexp": 16, "power": [16, 18], "straightforward": 16, "ch": [16, 18], "regex": [16, 18], "citrobact": 16, "werkmanii": 16, "younga": 16, "uba": 16, "spx": 16, "uba2009": 16, "rokubacterial": 16, "sp": [16, 17], "least": [16, 18], "digit": 16, "escherichia": 16, "sp002965065": 16, "sp005281345": 16, "equal": [16, 19, 20], "edit": 16, "trigger": 16, "editor": 16, "four": [16, 20], "regard": [16, 19, 20], "pure": 16, "obligatori": 16, "tree_layout": 16, "mytreelayout": 16, "append": [16, 19], "frame": 16, "treelayout_1": 16, "futher": 16, "modify_tree_styl": 16, "treestyle_1": 16, "mylegend": 16, "green": [16, 19, 20], "treestyle_legend": 16, "attributt": 16, "foreground": [16, 20], "thats": 16, "ff0000": [16, 20], "hex": 16, "0030c1": 16, "outline_line_color": 16, "border": [16, 20], "000000": [16, 20], "outline_line_width": 16, "outline_color": 16, "e5e5e5": 16, "outline_opac": 16, "vt_line_color": [16, 20], "verticl": 16, "hz_line_color": [16, 20], "hz_line_typ": [16, 20], "vt_line_typ": [16, 20], "pf": 16, "piexl": 16, "fo": 16, "triangle_node_styl": 16, "brown": [16, 20], "964b00": 16, "modify_node_styl": 16, "corner": 16, "nodestyle_triangl": 16, "must": [16, 19, 20], "leaf_styl": 16, "root_styl": 16, "nodestyle_differ": 16, "extern": [16, 19, 20], "outlinedfac": 16, "dengzq1234": 16, "ete4_galleri": 16, "around": [16, 20], "modify_face_posit": 16, "hola": [16, 20], "mundo": [16, 20], "faceposition_bottom": 16, "pile": [16, 20], "faceposition_align": 16, "recycl": [16, 20], "notabl": 16, "directli": [16, 19, 20], "faceposition_collaps": 16, "faceposition_al": 16, "config": [16, 20], "permit": [16, 20], "veri": [16, 19, 20], "top_textfac": 16, "courier": 16, "togeth": [16, 19], "bottom_textfac": 16, "modify_face_properti": 16, "faceproperties_textfac": 16, "sent": [16, 20], "wrap": 16, "modfii": 16, "insid": [16, 18], "vowel_node_layout": 16, "vowel": [16, 19, 20], "advance_layout": 16, "vowel_tree_styl": 16, "conost": 16, "combinedlayout_bas": 16, "vowel_color": 16, "conostant_color": 16, "vowel_node_s": 16, "conostant_node_s": 16, "ensur": [16, 20], "goe": 16, "addit": [16, 17, 18, 19], "super": [16, 20], "vowel_textfac": 16, "conostant_textfac": 16, "combinedlayout_object": 16, "a3": [16, 20], "b3": [16, 20], "b4": [16, 20], "c1": [16, 20], "c2": [16, 20], "c3": [16, 20], "nst1": [16, 20], "lightsteelblu": [16, 20], "nst2": [16, 20], "moccasin": [16, 20], "nst3": [16, 20], "darkseagreen": [16, 20], "nst4": [16, 20], "khaki": [16, 20], "n3": [16, 20], "n4": [16, 20], "ancestor_a": 16, "ancestor_b": 16, "ancestor_c": 16, "ancestor_d": 16, "get_tree_styl": 16, "get_background": 16, "bigger": 16, "node_background": [16, 20], "d1": 16, "d2": 16, "get_node_fac": 16, "lca_fac": 16, "white": [16, 20], "rotate_text": 16, "colorstrip": 16, "numer": [16, 17], "count": [16, 19], "randint": [16, 20], "layout_tree_styl": 16, "sample1": 16, "150": [16, 20], "layout_barplot": 16, "rect_fac": 16, "skyblu": 16, "barplot_layout": 16, "barplot": 16, "matplotlib": 16, "mpl": 16, "np": 16, "frequenc": 16, "darkr": [16, 20], "layout_heatmap": 16, "mincolor": 16, "maxcolor": 16, "maxval": 16, "max": [16, 20], "minval": 16, "mix": 16, "fade": 16, "linear": 16, "interpol": 16, "to_rgb": 16, "to_hex": 16, "get_heatmapfac": 16, "ratio": [16, 20], "gradient_color": 16, "print_frequnc": 16, "treefil": 16, "aln": 16, "faa": 16, "fastafil": 16, "phy003i7zj_chick": 16, "tmsqfnfssapagggfsfstpkt": 16, "name2seq": 16, "head": 16, "lstrip": 16, "rstrip": 16, "layout_alnface_grai": 16, "seq_fac": 16, "800": 16, "layout_alnface_compact": 16, "compactseq": [16, 20], "layout_seqfac": 16, "compact_aln": 16, "gray_aln": 16, "msa_layout": 16, "aqak": [16, 20], "ikgskkaikvfssa": [16, 20], "aperlqeygsiftda": [16, 20], "glqrrprhriqsk": [16, 20], "alqeklkdfpvcvstkpepeddaeeglgglpsn": [16, 20], "issvsslllfnttenlykkyvfldplag": [16, 20], "thvmlgaeteeklfdaplsiskreqleqqvpenyfyvpd": [16, 20], "lgqvpeidvpsylpdlpgiandlmyiadlgpgiapsapgtipelptfhtevaeplkvgelgsgmgagpgtp": [16, 20], "ahtpssldtphfvfqtykmgapplppstaapvgqgarqddssssaspsvqgaprevvdpsggwatllesir": [16, 20], "qaggigkaklrsmkerklekqqqkeqeqvratsqgghl": [16, 20], "msdlfnklvmrrkgisgkgpgagdgpggafa": [16, 20], "rvsdsipplpppqqpqaed": [16, 20], "mixed_motif": [16, 20], "rgradient": [16, 20], "arial": [16, 20], "long": [16, 19, 20], "clip": [16, 20], "101": [16, 20], "pink": [16, 20], "155": [16, 20], "180": 16, "purpl": [16, 19, 20], "160": [16, 20], "190": [16, 20], "24": 16, "yellow": [16, 19, 20], "191": [16, 20], "orang": [16, 20], "201": [16, 20], "250": [16, 20], "351": [16, 20], "370": [16, 20], "gold": [16, 20], "420": [16, 20], "simple_motif": [16, 20], "120": [16, 20], "300": [16, 20], "hello": [16, 18, 20], "box_motif": [16, 20], "ref": [16, 20], "85": [16, 20], "110": [16, 20], "125": [16, 20], "layout_domain": 16, "blank": [16, 20], "domain_layout": 16, "ncbi_taxonomi": 17, "gtdb_taxonomi": 17, "offer": 17, "vice": 17, "versa": 17, "fetch": 17, "comprehens": [17, 19], "organ": 17, "daili": 17, "portal": 17, "ftp": 17, "releas": 17, "dmp": 17, "taxon": 17, "taxonomyi": 17, "commonli": [17, 19], "signifi": 17, "entiti": 17, "genet": 17, "9606": 17, "On": 17, "hand": 17, "distribut": 17, "sqlite": 17, "fullfil": 17, "convers": [17, 20], "third": [17, 19], "parti": 17, "nick": 17, "youngblut": 17, "gtdb_to_taxdump": 17, "emploi": 17, "alreadi": [17, 18, 19, 20], "preprar": 17, "attempt": 17, "600mb": 17, "72mb": 17, "skip": 17, "answer": 17, "internet": 17, "fname": 17, "gtdb202dump": 17, "taxid2nam": 17, "9443": 17, "name2taxid": 17, "bacteria": 17, "629395": 17, "further": 17, "131567": 17, "2759": 17, "33154": 17, "33208": 17, "6072": 17, "33213": 17, "33511": 17, "7711": 17, "89593": 17, "7742": 17, "7776": 17, "117570": 17, "117571": 17, "8287": 17, "1338369": 17, "32523": 17, "32524": 17, "40674": 17, "32525": 17, "9347": 17, "1437010": 17, "314146": 17, "376913": 17, "314293": 17, "9526": 17, "314295": 17, "9604": 17, "207598": 17, "9605": 17, "cellular": 17, "eukaryota": 17, "opisthokonta": 17, "eumetazoa": 17, "bilateria": 17, "deuterostomia": 17, "chordata": 17, "craniata": 17, "vertebrata": 17, "gnathostomata": 17, "teleostomi": 17, "euteleostomi": 17, "sarcopterygii": 17, "dipnotetrapodomorpha": 17, "tetrapoda": 17, "amniota": 17, "mammalia": 17, "theria": 17, "eutheria": 17, "boreoeutheria": 17, "euarchontoglir": 17, "haplorrhini": 17, "simiiform": 17, "catarrhini": 17, "hominoidea": 17, "hominida": [17, 20], "hominina": 17, "doesn": [17, 18], "ve": 17, "facilit": [17, 19], "offici": 17, "recogn": 17, "easier": 17, "neanderthalensi": 17, "subsp": 17, "denisova": 17, "heidelbergensi": 17, "environment": 17, "sampl": 17, "subspeci": [17, 20], "2665952": 17, "2665953": 17, "1425170": 17, "unclassifi": 17, "2813598": 17, "2813599": 17, "f__thorarchaeacea": 17, "gb_gca_003662765": 17, "gb_gca_003662805": 17, "gb_gca_013138615": 17, "s__mp8t": 17, "sp002825535": 17, "sp003345545": 17, "s__tekir": 17, "sp004524435": 17, "g__mp8t": 17, "genu": [17, 20], "sp002825465": 17, "sp004524565": 17, "sp004524595": 17, "s__smtz1": 17, "83": 17, "sp011364985": 17, "g__smtz1": 17, "sp011365025": 17, "sp001563325": 17, "g__tekir": 17, "14": [17, 20], "sp004524445": 17, "g__shmx01": 17, "s__shmx01": 17, "sp008080745": 17, "s__owc5": 17, "sp003345595": 17, "g__owc5": 17, "f__tho": 17, "sp003345555": 17, "g__jacael01": 17, "s__jacael01": 17, "sp013388835": 17, "g__b65": 17, "g9": 17, "s__b65": 17, "sp003662765": 17, "sp001563335": 17, "sp011364905": 17, "sp001940705": 17, "sp004376265": 17, "sp002825515": 17, "g__wtck01": 17, "s__wtck01": 17, "sp013138615": 17, "smallest": 17, "9598": 17, "10090": 17, "7707": 17, "8782": 17, "dendrochirotida": 17, "subfamili": 17, "superord": 17, "av": 17, "p__huberarchaeota": 17, "o__peptococcal": 17, "f__korarchaeacea": 17, "phylum": 17, "d__archaea": 17, "superkingdom": 17, "p__thermoproteota": 17, "c__korarchaeia": 17, "o__korarchaeal": 17, "d__bacteria": 17, "p__firmicutes_b": 17, "c__peptococcia": 17, "sibl": 17, "rememb": 17, "bacteriovorax": 17, "stolpii": 17, "bdellovibrionota": 17, "3018035": 17, "bdellovibrio": 17, "bacteriovoru": 17, "ancylobact": 17, "aquaticu": 17, "prota": 17, "protb": 17, "namespac": 17, "gb_gca_020833055": 17, "gb_gca_003344655": 17, "rs_gcf_000019605": 17, "rs_gcf_003948265": 17, "s__korarchaeum": 17, "sp020833055": 17, "g__korarchaeum": 17, "sp003344655": 17, "cryptofilum": 17, "protc": 17, "protd": 17, "annotate_dict": 17, "gtdb_spcode": 17, "realat": 18, "impos": 18, "regular": 18, "imagin": 18, "treematch": 18, "tp": 18, "okai": 18, "ones": 18, "But": [18, 19], "seem": 18, "Will": [18, 19], "len": [18, 19, 20], "tripl": 18, "freeli": [18, 19], "distinguish": 18, "parenthesi": 18, "compil": 18, "feel": 18, "variant": 18, "incorrect": 18, "exist": [18, 19], "sup": 18, "getattr": 18, "legibl": 18, "nchildren": 18, "did": [18, 19], "know": 18, "tell": 18, "Of": [18, 19], "cours": [18, 19], "neg": 18, "beforehand": 18, "n2leav": 18, "final": [18, 19, 20], "consol": 18, "comfort": 18, "sparingli": 18, "enjoi": 18, "bye": 18, "construct": [18, 19], "expected_result": 18, "xx": 18, "nsearch": 18, "win": 18, "emul": 19, "design": [19, 20], "formal": 19, "acycl": 19, "down": 19, "superior": 19, "longest": 19, "downward": 19, "topmost": 19, "Being": 19, "begin": 19, "reach": 19, "bottommost": 19, "inner": 19, "portion": 19, "view": [19, 20], "compris": 19, "proper": 19, "analogi": 19, "term": 19, "subset": 19, "entail": 19, "consider": 19, "remain": 19, "constant": 19, "nest": 19, "parenthes": 19, "nevertheless": 19, "uncommon": 19, "variat": 19, "control": [19, 20], "definit": 19, "cool": 19, "high": 19, "With": [19, 20], "familiar": 19, "genes_tre": 19, "export": [19, 20], "notat": 19, "new_tre": 19, "success": 19, "practic": 19, "distinct": 19, "concept": 19, "review": 19, "moreov": 19, "latter": 19, "reliabl": 19, "bootstrap": 19, "syntax": 19, "conceptu": 19, "That": 19, "master": [19, 20], "rooted_tre": 19, "navig": 19, "explanatori": 19, "q": 19, "m": 19, "boolean": 19, "becom": 19, "cd": 19, "node2label": 19, "collapsed_leaf": 19, "sai": 19, "deepest": 19, "larger": 19, "abcd": 19, "efg": 19, "processable_nod": 19, "sometim": [19, 20], "along": 19, "node3": 19, "cannot": 19, "statement": 19, "search_by_s": 19, "40": 19, "handi": 19, "matches2": 19, "para": 19, "poli": 19, "phylet": 19, "inde": 19, "paraphylet": 19, "nor": 19, "polyphylet": 19, "signific": 19, "slowdown": 19, "instantan": 19, "node2leav": 19, "later": [19, 20], "ancestor_jfc": 19, "confid": 19, "nodetyp": 19, "loop": 19, "overwrit": 19, "is_vowel": 19, "aeiou": 19, "higher": 19, "long_branch_nod": 19, "precomput": 19, "conf": 19, "enclos": 19, "bracket": 19, "plain": 19, "www": 19, "phylosoft": 19, "adh2": 19, "adh1": 19, "05": 19, "adhi": 19, "nematod": 19, "adhx": 19, "insect": [19, 20], "adh4": 19, "adh3": 19, "fungi": 19, "tag": 19, "averag": 19, "max_rf": 19, "norm_rf": 19, "effective_tree_s": 19, "ref_edges_in_sourc": 19, "source_edges_in_ref": 19, "source_subtre": 19, "common_edg": 19, "source_edg": 19, "ref_edg": 19, "treeko_dist": 19, "metric": 19, "examin": 19, "discard": 19, "mention": 19, "parts_t1": 19, "parts_t2": 19, "total": 19, "tree2": 19, "were": 19, "tree1": 19, "hold": 19, "partial": 19, "Such": 19, "orphan": 19, "never": 19, "unless": 19, "ok": 19, "r1": 19, "r6": 19, "names_librari": 19, "r2": 19, "r3": 19, "r4": 19, "r5": 19, "disconnect": 19, "contrast": 19, "removed_nod": 19, "unnecessari": 19, "fact": 19, "serious": 19, "care": 19, "mistak": 19, "intric": 19, "serial": 19, "internal_1": 19, "internal_2": 19, "lose": 19, "_0_": 19, "1_": 19, "_2_": 19, "3_": 19, "arbitrarili": 19, "bifurc": 19, "realli": 19, "softwar": 19, "intact": 19, "recurs": 19, "polynod": 19, "techniqu": 19, "polar": 19, "basal": 19, "crucial": 19, "prior": 19, "determin": [19, 20], "differenti": 19, "moment": [19, 20], "obvious": 19, "brother": 19, "opposit": 19, "toplog": 19, "incorpor": 19, "occurr": 19, "instal": 20, "scratch": 20, "invok": 20, "raster": 20, "pictur": 20, "break": 20, "a4": 20, "183": 20, "circular_styl": 20, "se": 20, "increas": 20, "branch_vertical_margin": 20, "adjac": 20, "semi": 20, "circumfer": 20, "arc_start": 20, "clock": 20, "arc_span": 20, "sphere": 20, "nstyle": 20, "cccccc": 20, "replic": 20, "heatmap": 20, "profilefac": 20, "face_grid_tutori": 20, "apart": 20, "margin": 20, "margin_top": 20, "margin_right": 20, "margin_left": 20, "margin_bottom": 20, "inner_bord": 20, "lightgreen": 20, "abc_layout": 20, "probabl": 20, "get_example_tre": 20, "bold": 20, "0f0f0f": 20, "style1": 20, "style2": 20, "0000aa": 20, "__main__": 20, "400": 20, "root_opening_factor": 20, "dre": 20, "008339": 20, "300613": 20, "596401": 20, "640858": 20, "753230": 20, "182035": 20, "106234": 20, "271621": 20, "046042": 20, "953250": 20, "061813": 20, "110769": 20, "204419": 20, "973467": 20, "humanfac": 20, "mousefac": 20, "dogfac": 20, "chimpfac": 20, "fishfac": 20, "flyfac": 20, "readi": 20, "namefac": 20, "009000": 20, "danio": 20, "rerio": 20, "code2desc": 20, "zebrafish": 20, "known": 20, "tropic": 20, "freshwat": 20, "minnow": 20, "cyprinida": 20, "fli": 20, "diptera": 20, "possess": 20, "wing": 20, "mesothorax": 20, "halter": 20, "hind": 20, "metathorax": 20, "member": 20, "biped": 20, "chimpanze": 20, "colloqui": 20, "extant": 20, "ap": 20, "rodent": 20, "lupu": 20, "domest": 20, "wolf": 20, "canida": 20, "ordercarnivora": 20, "mylayout": 20, "longnamefac": 20, "multilin": 20, "descfac": 20, "enumer": 20, "aa0000": 20, "9db0cf": 20, "img_fac": 20, "600": 20, "weight": 20, "proport": 20, "royalblu": 20, "manual": 20, "bubble_map": 20, "treefac": 20, "small_t": 20, "laef": 20, "tree_fac": 20, "tree_width": 20, "seq_motif_fac": 20, "plai": 20, "colorsi": 20, "pyqt6": 20, "qtcore": 20, "qtgui": 20, "qcolor": 20, "qpen": 20, "qbrush": 20, "qtwidget": 20, "qgraphicsrectitem": 20, "qgraphicssimpletextitem": 20, "qgraphicsellipseitem": 20, "interactiveitem": 20, "setcursor": 20, "pointinghandcursor": 20, "setacceptshoverev": 20, "hoverenterev": 20, "hide": 20, "dynamicitemfac": 20, "setparentitem": 20, "zvalu": 20, "setzvalu": 20, "setbrush": 20, "settext": 20, "setrect": 20, "boundingrect": 20, "setvis": 20, "hoverleaveev": 20, "random_color": 20, "hue": 20, "rgb": 20, "luminos": 20, "satur": 20, "hls_to_rgb": 20, "02x": 20, "255": 20, "ugly_name_fac": 20, "qgraphicsitem": 20, "masteritem": 20, "doc": 20, "No": 20, "setpen": 20, "nopen": 20, "ellips": 20, "tw": 20, "th": 20, "setpo": 20, "master_li": 20, "itemfac": 20, "forward": 20}, "objects": {"ete4": [[10, 0, 1, "", "GTDBTaxa"], [10, 0, 1, "", "NCBITaxa"], [7, 0, 1, "", "PhyloTree"], [11, 0, 1, "", "Tree"]], "ete4.GTDBTaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_lineage"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.NCBITaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_fuzzy_name_translation"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.PhyloTree": [[7, 1, 1, "", "__init__"], [7, 1, 1, "", "annotate_gtdb_taxa"], [7, 1, 1, "", "annotate_ncbi_taxa"], [7, 1, 1, "", "collapse_lineage_specific_expansions"], [7, 1, 1, "", "get_age"], [7, 1, 1, "", "get_age_balanced_outgroup"], [7, 1, 1, "", "get_descendant_evol_events"], [7, 1, 1, "", "get_farthest_oldest_leaf"], [7, 1, 1, "", "get_farthest_oldest_node"], [7, 1, 1, "", "get_my_evol_events"], [7, 1, 1, "", "get_speciation_trees"], [7, 1, 1, "", "get_species"], [7, 1, 1, "", "iter_species"], [7, 1, 1, "", "link_to_alignment"], [7, 1, 1, "", "ncbi_compare"], [7, 1, 1, "", "reconcile"], [7, 1, 1, "", "set_species_naming_function"], [7, 2, 1, "", "species"], [7, 1, 1, "", "split_by_dups"], [7, 1, 1, "", "write"]], "ete4.Tree": [[11, 1, 1, "", "__init__"], [11, 1, 1, "", "add_child"], [11, 1, 1, "", "add_children"], [11, 1, 1, "", "add_face"], [11, 1, 1, "", "add_face_smartview"], [11, 1, 1, "", "add_face_treeview"], [11, 1, 1, "", "add_feature"], [11, 1, 1, "", "add_features"], [11, 1, 1, "", "add_prop"], [11, 1, 1, "", "add_props"], [11, 1, 1, "", "add_sister"], [11, 1, 1, "", "ancestors"], [11, 1, 1, "", "check_monophyly"], [11, 3, 1, "", "children"], [11, 3, 1, "", "collapsed_faces"], [11, 1, 1, "", "common_ancestor"], [11, 1, 1, "", "compare"], [11, 1, 1, "", "cophenetic_matrix"], [11, 1, 1, "", "copy"], [11, 1, 1, "", "del_feature"], [11, 1, 1, "", "del_prop"], [11, 1, 1, "", "delete"], [11, 1, 1, "", "descendants"], [11, 1, 1, "", "describe"], [11, 1, 1, "", "detach"], [11, 3, 1, "", "dist"], [11, 1, 1, "", "edges"], [11, 1, 1, "", "expand_polytomies"], [11, 1, 1, "", "explore"], [11, 3, 1, "", "faces"], [11, 1, 1, "", "from_parent_child_table"], [11, 1, 1, "", "from_skbio"], [11, 1, 1, "", "get_cached_content"], [11, 1, 1, "", "get_children"], [11, 1, 1, "", "get_closest_leaf"], [11, 1, 1, "", "get_distance"], [11, 1, 1, "", "get_farthest_leaf"], [11, 1, 1, "", "get_farthest_node"], [11, 1, 1, "", "get_midpoint_outgroup"], [11, 1, 1, "", "get_monophyletic"], [11, 1, 1, "", "get_prop"], [11, 1, 1, "", "get_sisters"], [11, 1, 1, "", "get_topology_id"], [11, 3, 1, "", "id"], [11, 2, 1, "", "img_style"], [11, 1, 1, "", "init_from_ete"], [11, 1, 1, "", "init_from_newick"], [11, 2, 1, "", "is_collapsed"], [11, 2, 1, "", "is_initialized"], [11, 3, 1, "", "is_leaf"], [11, 1, 1, "", "is_monophyletic"], [11, 3, 1, "", "is_root"], [11, 1, 1, "", "iter_prepostorder"], [11, 1, 1, "", "ladderize"], [11, 1, 1, "", "leaf_names"], [11, 1, 1, "", "leaves"], [11, 3, 1, "", "level"], [11, 1, 1, "", "lineage"], [11, 3, 1, "", "name"], [11, 1, 1, "", "pop_child"], [11, 1, 1, "", "populate"], [11, 3, 1, "", "props"], [11, 1, 1, "", "prune"], [11, 1, 1, "", "remove_child"], [11, 1, 1, "", "remove_children"], [11, 1, 1, "", "remove_sister"], [11, 1, 1, "", "render"], [11, 1, 1, "", "resolve_polytomy"], [11, 1, 1, "", "reverse_children"], [11, 1, 1, "", "robinson_foulds"], [11, 3, 1, "", "root"], [11, 1, 1, "", "search_ancestors"], [11, 1, 1, "", "search_descendants"], [11, 1, 1, "", "search_leaves_by_name"], [11, 1, 1, "", "search_nodes"], [11, 1, 1, "", "set_outgroup"], [11, 1, 1, "", "set_style"], [11, 1, 1, "", "show"], [11, 3, 1, "", "size"], [11, 2, 1, "", "sm_style"], [11, 1, 1, "", "sort_descendants"], [11, 1, 1, "", "standardize"], [11, 3, 1, "", "support"], [11, 1, 1, "", "swap_children"], [11, 1, 1, "", "to_str"], [11, 1, 1, "", "to_ultrametric"], [11, 1, 1, "", "traverse"], [11, 1, 1, "", "unroot"], [11, 3, 1, "", "up"], [11, 1, 1, "", "write"]], "ete4.clustering": [[4, 4, 0, "-", "clustertree"]], "ete4.clustering.clustertree": [[4, 0, 1, "", "ClusterTree"]], "ete4.clustering.clustertree.ClusterTree": [[4, 1, 1, "", "__init__"], [4, 2, 1, "", "deviation"], [4, 1, 1, "", "get_dunn"], [4, 1, 1, "", "get_silhouette"], [4, 2, 1, "", "intercluster_dist"], [4, 2, 1, "", "intracluster_dist"], [4, 1, 1, "", "leaf_profiles"], [4, 1, 1, "", "link_to_arraytable"], [4, 2, 1, "", "profile"], [4, 1, 1, "", "set_distance_function"], [4, 2, 1, "", "silhouette"]], "ete4.core": [[5, 4, 0, "-", "operations"], [8, 4, 0, "-", "seqgroup"]], "ete4.core.operations": [[5, 0, 1, "", "Walker"], [5, 5, 1, "", "add_branch_values"], [5, 5, 1, "", "add_leaf_names"], [5, 5, 1, "", "assert_root_consistency"], [5, 5, 1, "", "common_ancestor"], [5, 5, 1, "", "create_dichotomic_sister"], [5, 5, 1, "", "farthest"], [5, 5, 1, "", "farthest_descendant"], [5, 5, 1, "", "insert_intermediate"], [5, 5, 1, "", "interchange_references"], [5, 5, 1, "", "join_branch"], [5, 5, 1, "", "ladderize"], [5, 5, 1, "", "make_name"], [5, 5, 1, "", "midpoint"], [5, 5, 1, "", "move"], [5, 5, 1, "", "populate"], [5, 5, 1, "", "populate_uniform"], [5, 5, 1, "", "populate_yule"], [5, 5, 1, "", "rehang"], [5, 5, 1, "", "remove"], [5, 5, 1, "", "resolve_polytomy"], [5, 5, 1, "", "root_at"], [5, 5, 1, "", "set_midpoint_outgroup"], [5, 5, 1, "", "set_outgroup"], [5, 5, 1, "", "sort"], [5, 5, 1, "", "swap_props"], [5, 5, 1, "", "to_dendrogram"], [5, 5, 1, "", "to_ultrametric"], [5, 5, 1, "", "traverse"], [5, 5, 1, "", "traverse_bfs"], [5, 5, 1, "", "unroot"], [5, 5, 1, "", "update_size"], [5, 5, 1, "", "update_sizes_all"], [5, 5, 1, "", "update_sizes_from"], [5, 5, 1, "", "walk"]], "ete4.core.operations.Walker": [[5, 1, 1, "", "add_next_branch"], [5, 2, 1, "", "first_visit"], [5, 1, 1, "", "go_back"], [5, 2, 1, "", "has_unvisited_branches"], [5, 2, 1, "", "node"], [5, 2, 1, "", "node_id"]], "ete4.core.seqgroup": [[8, 0, 1, "", "SeqGroup"]], "ete4.core.seqgroup.SeqGroup": [[8, 1, 1, "", "__init__"], [8, 1, 1, "", "get_entries"], [8, 1, 1, "", "get_seq"], [8, 1, 1, "", "iter_entries"], [8, 1, 1, "", "set_seq"], [8, 1, 1, "", "write"]], "ete4.parser": [[6, 4, 0, "-", "newick"], [6, 4, 0, "-", "nexus"]], "ete4.parser.newick": [[6, 6, 1, "", "NewickError"], [6, 5, 1, "", "content_repr"], [6, 5, 1, "", "dump"], [6, 5, 1, "", "dumps"], [6, 5, 1, "", "error"], [6, 5, 1, "", "get_extended_props"], [6, 5, 1, "", "get_props"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"], [6, 5, 1, "", "make_parser"], [6, 5, 1, "", "prop_repr"], [6, 5, 1, "", "quote"], [6, 5, 1, "", "read_content"], [6, 5, 1, "", "read_nodes"], [6, 5, 1, "", "repr_short"], [6, 5, 1, "", "skip_quoted_name"], [6, 5, 1, "", "skip_spaces_and_comments"], [6, 5, 1, "", "unquote"]], "ete4.parser.nexus": [[6, 6, 1, "", "NexusError"], [6, 5, 1, "", "apply_translations"], [6, 5, 1, "", "get_commands"], [6, 5, 1, "", "get_section"], [6, 5, 1, "", "get_sections"], [6, 5, 1, "", "get_trees"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"]], "ete4.phylo": [[7, 0, 1, "", "EvolEvent"]], "ete4.smartview.gui": [[9, 4, 0, "-", "server"]], "ete4.smartview.gui.server": [[9, 0, 1, "", "GlobalStuff"], [9, 0, 1, "", "TreeData"], [9, 5, 1, "", "activate_clade"], [9, 5, 1, "", "activate_node"], [9, 5, 1, "", "add_tree"], [9, 5, 1, "", "add_trees_from_request"], [9, 5, 1, "", "callback"], [9, 5, 1, "", "change_selection_name"], [9, 5, 1, "", "copy_style"], [9, 5, 1, "", "deactivate_clade"], [9, 5, 1, "", "deactivate_node"], [9, 5, 1, "", "del_tree"], [9, 5, 1, "", "find_node"], [9, 5, 1, "", "get_active_clade"], [9, 5, 1, "", "get_active_clades"], [9, 5, 1, "", "get_command_search"], [9, 5, 1, "", "get_drawer"], [9, 5, 1, "", "get_eval_search"], [9, 5, 1, "", "get_layouts"], [9, 5, 1, "", "get_layouts_from_getters"], [9, 5, 1, "", "get_newick"], [9, 5, 1, "", "get_next_available_port"], [9, 5, 1, "", "get_nodes_info"], [9, 5, 1, "", "get_parents"], [9, 5, 1, "", "get_parser"], [9, 5, 1, "", "get_search_function"], [9, 5, 1, "", "get_selection_info"], [9, 5, 1, "", "get_selections"], [9, 5, 1, "", "get_stats"], [9, 5, 1, "", "get_tid"], [9, 5, 1, "", "get_topological_search"], [9, 5, 1, "", "get_trees_from_file"], [9, 5, 1, "", "get_trees_from_form"], [9, 5, 1, "", "get_trees_from_nexus_or_newick"], [9, 5, 1, "", "initialize"], [9, 5, 1, "", "initialize_tree_style"], [9, 5, 1, "", "json_error"], [9, 5, 1, "", "load_tree"], [9, 5, 1, "", "load_tree_from_newick"], [9, 5, 1, "", "maintenance"], [9, 5, 1, "", "make_name"], [9, 5, 1, "", "nice_html"], [9, 5, 1, "", "open_browser_window"], [9, 5, 1, "", "prune_by_selection"], [9, 5, 1, "", "remove_active"], [9, 5, 1, "", "remove_active_clade"], [9, 5, 1, "", "remove_search"], [9, 5, 1, "", "remove_selection"], [9, 5, 1, "", "req_json"], [9, 5, 1, "", "retrieve_layouts"], [9, 5, 1, "", "retrieve_tree_data"], [9, 5, 1, "", "run_smartview"], [9, 5, 1, "", "safer_eval"], [9, 5, 1, "", "search_to_selection"], [9, 5, 1, "", "sort"], [9, 5, 1, "", "store_active"], [9, 5, 1, "", "store_search"], [9, 5, 1, "", "store_selection"], [9, 5, 1, "", "touch_and_get"], [9, 5, 1, "", "unselect_node"], [9, 5, 1, "", "update_app_available_layouts"], [9, 5, 1, "", "update_layouts"], [9, 5, 1, "", "update_node_props"], [9, 5, 1, "", "update_node_style"], [9, 5, 1, "", "update_selection"]], "ete4.smartview.gui.server.TreeData": [[9, 1, 1, "", "__init__"], [9, 3, 1, "", "active"], [9, 3, 1, "", "exclude_props"], [9, 3, 1, "", "include_props"], [9, 3, 1, "", "initialized"], [9, 3, 1, "", "layouts"], [9, 3, 1, "", "name"], [9, 3, 1, "", "nodestyles"], [9, 3, 1, "", "searches"], [9, 3, 1, "", "selected"], [9, 3, 1, "", "style"], [9, 3, 1, "", "timer"], [9, 3, 1, "", "tree"], [9, 3, 1, "", "ultrametric"]], "ete4.smartview.renderer": [[9, 4, 0, "-", "draw_helpers"], [9, 4, 0, "-", "drawer"], [9, 4, 0, "-", "face_positions"], [9, 4, 0, "-", "faces"], [9, 4, 0, "-", "nodestyle"], [9, 4, 0, "-", "treelayout"], [9, 4, 0, "-", "treestyle"]], "ete4.smartview.renderer.draw_helpers": [[9, 0, 1, "", "Box"], [9, 0, 1, "", "Padding"], [9, 5, 1, "", "cartesian"], [9, 5, 1, "", "circumasec"], [9, 5, 1, "", "circumrect"], [9, 5, 1, "", "clip_angles"], [9, 5, 1, "", "draw_arc"], [9, 5, 1, "", "draw_array"], [9, 5, 1, "", "draw_arrow"], [9, 5, 1, "", "draw_circle"], [9, 5, 1, "", "draw_ellipse"], [9, 5, 1, "", "draw_html"], [9, 5, 1, "", "draw_img"], [9, 5, 1, "", "draw_line"], [9, 5, 1, "", "draw_nodebox"], [9, 5, 1, "", "draw_outline"], [9, 5, 1, "", "draw_rect"], [9, 5, 1, "", "draw_rhombus"], [9, 5, 1, "", "draw_slice"], [9, 5, 1, "", "draw_text"], [9, 5, 1, "", "draw_triangle"], [9, 5, 1, "", "first_value"], [9, 5, 1, "", "get_line_type"], [9, 5, 1, "", "get_xs"], [9, 5, 1, "", "get_ys"], [9, 5, 1, "", "intersects_angles"], [9, 5, 1, "", "intersects_box"], [9, 5, 1, "", "intersects_segment"], [9, 5, 1, "", "split_thru_negative_xaxis"], [9, 5, 1, "", "summary"]], "ete4.smartview.renderer.draw_helpers.Box": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"], [9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.draw_helpers.Padding": [[9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.drawer": [[9, 0, 1, "", "Active"], [9, 0, 1, "", "Drawer"], [9, 0, 1, "", "DrawerAlignCircFaces"], [9, 0, 1, "", "DrawerAlignRectFaces"], [9, 0, 1, "", "DrawerCirc"], [9, 0, 1, "", "DrawerCircFaces"], [9, 0, 1, "", "DrawerRect"], [9, 0, 1, "", "DrawerRectFaces"], [9, 0, 1, "", "Size"], [9, 0, 1, "", "TreeActive"], [9, 5, 1, "", "dist"], [9, 5, 1, "", "drawn_size"], [9, 5, 1, "", "get_asec"], [9, 5, 1, "", "get_drawers"], [9, 5, 1, "", "get_empty_active"], [9, 5, 1, "", "get_rect"], [9, 5, 1, "", "make_box"], [9, 5, 1, "", "safe_string"], [9, 5, 1, "", "stack"]], "ete4.smartview.renderer.drawer.Active": [[9, 3, 1, "", "parents"], [9, 3, 1, "", "results"]], "ete4.smartview.renderer.drawer.Drawer": [[9, 3, 1, "", "COLLAPSE_SIZE"], [9, 3, 1, "", "MIN_SIZE"], [9, 3, 1, "", "NPANELS"], [9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "draw_aligned_headers"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_content"], [9, 1, 1, "", "draw_node"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_active_children"], [9, 1, 1, "", "get_collapsed_node"], [9, 1, 1, "", "get_outline"], [9, 1, 1, "", "get_popup_props"], [9, 1, 1, "", "get_selected_children"], [9, 1, 1, "", "is_fully_collapsed"], [9, 1, 1, "", "on_first_visit"], [9, 1, 1, "", "on_last_visit"]], "ete4.smartview.renderer.drawer.DrawerAlignCircFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerAlignRectFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerCirc": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerCircFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.DrawerRect": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerRectFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.Size": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"]], "ete4.smartview.renderer.drawer.TreeActive": [[9, 3, 1, "", "clades"], [9, 3, 1, "", "nodes"]], "ete4.smartview.renderer.face_positions": [[9, 0, 1, "", "AlignedGrid"], [9, 0, 1, "", "Grid"], [9, 5, 1, "", "make_faces"]], "ete4.smartview.renderer.face_positions.AlignedGrid": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.face_positions.Grid": [[9, 1, 1, "", "add_face"]], "ete4.smartview.renderer.faces": [[9, 0, 1, "", "AlignLinkFace"], [9, 0, 1, "", "AlignmentFace"], [9, 0, 1, "", "ArrowFace"], [9, 0, 1, "", "AttrFace"], [9, 0, 1, "", "CircleFace"], [9, 0, 1, "", "Face"], [9, 0, 1, "", "HTMLFace"], [9, 0, 1, "", "ImgFace"], [9, 0, 1, "", "LegendFace"], [9, 0, 1, "", "OutlineFace"], [9, 0, 1, "", "PieChartFace"], [9, 0, 1, "", "RectFace"], [9, 0, 1, "", "ScaleFace"], [9, 0, 1, "", "SelectedCircleFace"], [9, 0, 1, "", "SelectedFace"], [9, 0, 1, "", "SelectedRectFace"], [9, 0, 1, "", "SeqFace"], [9, 0, 1, "", "SeqMotifFace"], [9, 0, 1, "", "StackedBarFace"], [9, 0, 1, "", "TextFace"]], "ete4.smartview.renderer.faces.AlignLinkFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.AlignmentFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_blocks"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "get_seq"]], "ete4.smartview.renderer.faces.ArrowFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 2, 1, "", "orientation"]], "ete4.smartview.renderer.faces.AttrFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_content"]], "ete4.smartview.renderer.faces.CircleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.Face": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "compute_fsize"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "get_content"], [9, 1, 1, "", "in_aligned_viewport"]], "ete4.smartview.renderer.faces.HTMLFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ImgFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.LegendFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.OutlineFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.PieChartFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_pie"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.RectFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ScaleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SelectedCircleFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedRectFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SeqFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SeqMotifFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_regions"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.faces.StackedBarFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.TextFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.layouts": [[9, 4, 0, "-", "context_layouts"], [9, 4, 0, "-", "default_layouts"], [9, 4, 0, "-", "domain_layouts"], [9, 4, 0, "-", "eggnog6_layouts"], [9, 4, 0, "-", "etecompare_layouts"], [9, 4, 0, "-", "evocell_layouts"], [9, 4, 0, "-", "evol_events_layouts"], [9, 4, 0, "-", "ncbi_taxonomy_layouts"], [9, 4, 0, "-", "phylocloud_egg5_layouts"], [9, 4, 0, "-", "seq_layouts"], [9, 4, 0, "-", "spongilla_layouts"], [9, 4, 0, "-", "staple_layouts"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, 0, 1, "", "LayoutGenomicContext"]], "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_context"], [9, 1, 1, "", "get_tooltip"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, 0, 1, "", "LayoutBranchLength"], [9, 0, 1, "", "LayoutBranchSupport"], [9, 0, 1, "", "LayoutLeafName"], [9, 0, 1, "", "LayoutNumberLeaves"], [9, 0, 1, "", "LayoutOutline"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, 0, 1, "", "LayoutBestName"], [9, 0, 1, "", "LayoutBigg"], [9, 0, 1, "", "LayoutCard"], [9, 0, 1, "", "LayoutCazy"], [9, 0, 1, "", "LayoutEvolEvents"], [9, 0, 1, "", "LayoutKeggEnzyme"], [9, 0, 1, "", "LayoutKeggModule"], [9, 0, 1, "", "LayoutKeggNumber"], [9, 0, 1, "", "LayoutKeggPathway"], [9, 0, 1, "", "LayoutLastCommonAncestor"], [9, 0, 1, "", "LayoutPdb"], [9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutProteinName"], [9, 0, 1, "", "LayoutScientificName"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, 0, 1, "", "LayoutEteDiffDistance"]], "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, 0, 1, "", "LayoutHumanOGs"], [9, 0, 1, "", "LayoutUCSC"], [9, 0, 1, "", "LayoutUCSCtrans"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, 0, 1, "", "LayoutEvolEvents"]], "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, 0, 1, "", "LayoutLastCommonAncestor"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, 5, 1, "", "get_layout_evoltype"], [9, 5, 1, "", "get_layout_gnames"], [9, 5, 1, "", "get_layout_lca_rects"], [9, 5, 1, "", "get_layout_ogs_egg5"], [9, 5, 1, "", "get_layout_sciname"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, 0, 1, "", "LayoutAlignment"]], "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_seq"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, 0, 1, "", "LayoutAutoName"], [9, 0, 1, "", "LayoutCuratedName"], [9, 0, 1, "", "LayoutEukOgs"], [9, 0, 1, "", "LayoutPreferredName"], [9, 0, 1, "", "LayoutSciName"], [9, 0, 1, "", "LayoutSeeds"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, 0, 1, "", "LayoutBarplot"]], "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.nodestyle": [[9, 0, 1, "", "NodeStyle"]], "ete4.smartview.renderer.nodestyle.NodeStyle": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "init"]], "ete4.smartview.renderer.treelayout": [[9, 0, 1, "", "TreeLayout"], [9, 5, 1, "", "cased_name"]], "ete4.smartview.renderer.treelayout.TreeLayout": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.treestyle": [[9, 0, 1, "", "TreeStyle"]], "ete4.smartview.renderer.treestyle.TreeStyle": [[9, 1, 1, "", "__init__"], [9, 2, 1, "", "active_face"], [9, 2, 1, "", "active_face_pos"], [9, 1, 1, "", "add_legend"], [9, 2, 1, "", "aligned_panel_footer"], [9, 2, 1, "", "aligned_panel_header"], [9, 1, 1, "", "get_legend"], [9, 2, 1, "", "selected_face"], [9, 2, 1, "", "selected_face_pos"]], "ete4.treematcher": [[12, 4, 0, "-", "treematcher"]], "ete4.treematcher.treematcher": [[12, 0, 1, "", "TreePattern"], [12, 5, 1, "", "match"], [12, 5, 1, "", "safer_eval"], [12, 5, 1, "", "search"]], "ete4.treematcher.treematcher.TreePattern": [[12, 1, 1, "", "__init__"], [12, 1, 1, "", "match"], [12, 1, 1, "", "search"]], "": [[13, 4, 0, "-", "treeview"]]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:property", "3": "py:attribute", "4": "py:module", "5": "py:function", "6": "py:exception"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "property", "Python property"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "module", "Python module"], "5": ["py", "function", "Python function"], "6": ["py", "exception", "Python exception"]}, "titleterms": {"about": 0, "highlight": 0, "tool": 0, "us": [0, 1, 17], "et": [0, 1, 2, 19], "relat": 0, "link": [0, 15], "resourc": 0, "frequent": 1, "ask": 1, "question": 1, "content": [1, 2, 9, 13, 15, 16, 17, 18, 19, 20], "gener": 1, "how": [1, 19], "do": 1, "i": 1, "tree": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "brows": [1, 19], "find": [1, 19], "leaf": [1, 16, 20], "its": 1, "name": [1, 16, 20], "visit": 1, "all": [1, 19], "node": [1, 15, 16, 18, 19, 20], "within": [1, 19, 20], "can": 1, "control": [1, 15, 16], "order": 1, "which": 1, "ar": 1, "read": [1, 19], "write": [1, 19], "load": 1, "intern": 1, "support": [1, 16, 20], "export": 1, "annot": [1, 16, 17, 19], "newick": [1, 6, 19], "format": 1, "visual": [1, 15, 16, 20], "draw": [1, 9, 16, 20], "circular": [1, 20], "imag": [1, 20], "svg": 1, "veri": 1, "unbalanc": 1, "branch": [1, 16, 19, 20], "improv": 1, "welcom": 2, "": [2, 16, 19], "document": 2, "indic": 2, "tabl": 2, "refer": 3, "guid": 3, "cluster": 4, "oper": [5, 19], "parser": 6, "nexu": 6, "phylogenet": [7, 15, 20], "phylotre": 7, "evolev": 7, "multipl": [8, 15, 16], "sequenc": [8, 15, 16, 20], "align": [8, 15, 16], "seqgroup": 8, "smartview": 9, "web": [9, 16], "graphic": [9, 13], "server": 9, "render": [9, 20], "drawer": 9, "helper": 9, "face": [9, 13, 16, 20], "posit": [9, 16, 20], "nodestyl": [9, 13], "treelayout": 9, "treestyl": [9, 13], "layout": [9, 16, 20], "context": 9, "default": 9, "domain": [9, 16, 20], "eggnog6": 9, "etecompar": 9, "evocel": 9, "evol_ev": 9, "ncbi_taxonomi": 9, "phylocloud_egg5": 9, "seq": 9, "spongilla": 9, "stapl": 9, "taxonomi": [10, 17], "databas": [10, 17], "ncbitaxa": 10, "gtdbtaxa": 10, "main": 11, "class": 11, "matcher": [12, 18], "treeview": 13, "qt": [13, 20], "tutori": 14, "overview": [15, 16, 17, 20], "ad": 15, "taxonom": 15, "inform": [15, 17], "automat": [15, 17], "speci": [15, 17], "info": 15, "custom": [15, 16, 19, 20], "manual": 15, "detect": 15, "evolutionari": 15, "event": 15, "overlap": 15, "so": 15, "algorithm": 15, "reconcili": 15, "A": [15, 18], "closer": 15, "look": 15, "object": [15, 16], "rel": [15, 19], "date": 15, "implement": 15, "root": [15, 19], "outgroup": [15, 19], "work": [15, 19], "duplic": [15, 19], "gene": 15, "famili": 15, "treeko": 15, "split": 15, "collaps": [15, 16, 19], "specif": 15, "explor": 16, "interact": [16, 20], "standalon": 16, "script": 16, "session": 16, "verbos": 16, "mode": 16, "show": [16, 20], "length": [16, 20], "properti": [16, 19, 20], "pop": 16, "up": [16, 17], "panel": 16, "1": 16, "tab": 16, "overral": 16, "download": 16, "2": 16, "search": [16, 19], "select": 16, "simpl": [16, 18], "regular": 16, "express": [16, 18], "topolog": 16, "exampl": [16, 18], "possibl": 16, "match": [16, 19], "3": 16, "advanc": [16, 19], "aspect": [16, 20], "style": [16, 20], "add": [16, 20], "legend": [16, 20], "clade": 16, "function": [16, 19, 20], "combin": [16, 20], "fix": [16, 20], "defin": 16, "background": [16, 20], "color": 16, "strip": 16, "outlin": 16, "bar": 16, "plot": 16, "heatmap": 16, "differ": 17, "between": [17, 19, 20], "ncbi": 17, "gtdb": 17, "ete4": 17, "set": 17, "local": 17, "copi": [17, 19], "get": [17, 19], "taxid": 17, "descend": [17, 19], "taxa": 17, "topologi": [17, 18, 19], "onli": 18, "less": 18, "outsid": 18, "variabl": 18, "from": [18, 19], "test": 18, "suit": 18, "structur": 19, "creat": [19, 20], "understand": 19, "basic": 19, "attribut": 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"]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest"]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant"]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit"]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back"]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches"]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate"]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references"]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch"]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize"]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name"]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint"]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move"]], "node (walker property)": [[5, "ete4.core.operations.Walker.node"]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id"]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate"]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform"]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule"]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang"]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove"]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy"]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at"]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup"]], "set_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_outgroup"]], "sort() (in module ete4.core.operations)": [[5, "ete4.core.operations.sort"]], "swap_props() (in module ete4.core.operations)": [[5, "ete4.core.operations.swap_props"]], "to_dendrogram() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_dendrogram"]], "to_ultrametric() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_ultrametric"]], "traverse() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse"]], "traverse_bfs() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse_bfs"]], "unroot() (in module ete4.core.operations)": [[5, "ete4.core.operations.unroot"]], "update_size() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_size"]], "update_sizes_all() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_all"]], "update_sizes_from() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_from"]], "walk() (in module ete4.core.operations)": [[5, "ete4.core.operations.walk"]], "newickerror": [[6, "ete4.parser.newick.NewickError"]], "nexuserror": [[6, "ete4.parser.nexus.NexusError"]], "apply_translations() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.apply_translations"]], "content_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.content_repr"]], "dump() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dump"]], "dumps() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dumps"]], "error() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.error"]], "ete4.parser.newick": [[6, "module-ete4.parser.newick"]], "ete4.parser.nexus": [[6, "module-ete4.parser.nexus"]], "get_commands() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_commands"]], "get_extended_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_extended_props"]], "get_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_props"]], "get_section() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_section"]], "get_sections() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_sections"]], "get_trees() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_trees"]], "load() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.load"]], "load() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.load"]], "loads() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.loads"]], "loads() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.loads"]], "make_parser() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.make_parser"]], "prop_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.prop_repr"]], "quote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.quote"]], "read_content() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_content"]], "read_nodes() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_nodes"]], "repr_short() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.repr_short"]], "skip_quoted_name() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_quoted_name"]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_spaces_and_comments"]], "unquote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.unquote"]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree"]], "__init__() (phylotree method)": [[7, "ete4.PhyloTree.__init__"]], "annotate_gtdb_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[7, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[7, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[7, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries"]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq"]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries"]], "set_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.set_seq"]], "write() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.write"]], "active (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Active"]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace"]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid"]], "alignmentface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignmentFace"]], "arrowface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ArrowFace"]], "attrface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AttrFace"]], "box (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Box"]], "collapse_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE"]], "circleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.CircleFace"]], "drawer (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Drawer"]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces"]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces"]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc"]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces"]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRect"]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces"]], "face (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.Face"]], "globalstuff (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.GlobalStuff"]], "grid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.Grid"]], "htmlface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.HTMLFace"]], "imgface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ImgFace"]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment"]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName"]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot"]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName"]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg"]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength"]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport"]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard"]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy"]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName"]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance"]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs"]], "layoutevolevents (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents"]], "layoutevolevents (class in ete4.smartview.renderer.layouts.evol_events_layouts)": [[9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents"]], "layoutgenomiccontext (class in ete4.smartview.renderer.layouts.context_layouts)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext"]], "layouthumanogs (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs"]], "layoutkeggenzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme"]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule"]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber"]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway"]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor"]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor"]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName"]], "layoutnumberleaves (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves"]], "layoutoutline (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline"]], "layoutpdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb"]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains"]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains"]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName"]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName"]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName"]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName"]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains"]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC"]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans"]], "legendface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.LegendFace"]], "min_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE"]], "npanels (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.NPANELS"]], "npanels (draweraligncircfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS"]], "npanels (draweralignrectfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS"]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle"]], "outlineface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.OutlineFace"]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Padding"]], "piechartface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.PieChartFace"]], "rectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.RectFace"]], "scaleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ScaleFace"]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace"]], "selectedface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedFace"]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace"]], "seqface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqFace"]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace"]], "size (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Size"]], "stackedbarface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.StackedBarFace"]], "type (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.TYPE"]], "type (drawercirc attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.TYPE"]], "type (drawerrect attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.TYPE"]], "textface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.TextFace"]], "treeactive (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.TreeActive"]], "treedata (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.TreeData"]], "treelayout (class in ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout"]], "treestyle (class in ete4.smartview.renderer.treestyle)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle"]], "__init__() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.__init__"]], "__init__() (alignedgrid method)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid.__init__"]], "__init__() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.__init__"]], "__init__() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.__init__"]], "__init__() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.__init__"]], "__init__() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.__init__"]], "__init__() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.__init__"]], "__init__() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.__init__"]], "__init__() (face method)": [[9, "ete4.smartview.renderer.faces.Face.__init__"]], "__init__() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.__init__"]], "__init__() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.__init__"]], "__init__() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.__init__"]], "__init__() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.__init__"]], "__init__() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.__init__"]], "__init__() (layoutbestname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName.__init__"]], "__init__() (layoutbigg method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg.__init__"]], "__init__() (layoutbranchlength method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength.__init__"]], "__init__() (layoutbranchsupport method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport.__init__"]], "__init__() (layoutcard method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard.__init__"]], "__init__() (layoutcazy method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy.__init__"]], "__init__() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.__init__"]], "__init__() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.__init__"]], "__init__() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.__init__"]], "__init__() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.__init__"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.__init__"]], "__init__() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.__init__"]], "__init__() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.__init__"]], "__init__() (layoutkeggenzyme method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme.__init__"]], "__init__() (layoutkeggmodule method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule.__init__"]], "__init__() (layoutkeggnumber method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber.__init__"]], "__init__() (layoutkeggpathway method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway.__init__"]], "__init__() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.__init__"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.__init__"]], "__init__() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.__init__"]], "__init__() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.__init__"]], "__init__() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.__init__"]], "__init__() (layoutpdb method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb.__init__"]], "__init__() (layoutpfamdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains.__init__"], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains.__init__"]], "__init__() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.__init__"]], "__init__() (layoutproteinname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName.__init__"]], "__init__() (layoutsciname method)": [[9, "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, "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_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"]], "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_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data"]], "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, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop"]], "delete() (tree method)": [[11, "ete4.Tree.delete"]], "descendants() (tree method)": [[11, "ete4.Tree.descendants"]], "describe() (tree method)": [[11, "ete4.Tree.describe"]], "detach() (tree method)": [[11, "ete4.Tree.detach"]], "dist (tree attribute)": [[11, "ete4.Tree.dist"]], "edges() (tree method)": [[11, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies"]], "explore() (tree method)": [[11, "ete4.Tree.explore"]], "faces (tree attribute)": [[11, "ete4.Tree.faces"]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table"]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio"]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content"]], "get_children() (tree method)": [[11, "ete4.Tree.get_children"]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf"]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance"]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf"]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node"]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup"]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic"]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop"]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters"]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id"]], "id (tree attribute)": [[11, "ete4.Tree.id"]], "img_style (tree property)": [[11, "ete4.Tree.img_style"]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete"]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick"]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed"]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized"]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf"]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic"]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root"]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder"]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize"]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names"]], "leaves() (tree method)": [[11, "ete4.Tree.leaves"]], "level (tree attribute)": [[11, "ete4.Tree.level"]], "lineage() (tree method)": [[11, "ete4.Tree.lineage"]], "name (tree attribute)": [[11, "ete4.Tree.name"]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child"]], "populate() (tree method)": [[11, "ete4.Tree.populate"]], "props (tree attribute)": [[11, "ete4.Tree.props"]], "prune() (tree method)": [[11, "ete4.Tree.prune"]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child"]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children"]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister"]], "render() (tree method)": [[11, "ete4.Tree.render"]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy"]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children"]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds"]], "root (tree attribute)": [[11, "ete4.Tree.root"]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors"]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants"]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name"]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes"]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup"]], "set_style() (tree method)": [[11, "ete4.Tree.set_style"]], "show() (tree method)": [[11, "ete4.Tree.show"]], "size (tree attribute)": [[11, "ete4.Tree.size"]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style"]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants"]], "standardize() (tree method)": [[11, "ete4.Tree.standardize"]], "support (tree attribute)": [[11, "ete4.Tree.support"]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children"]], "to_str() (tree method)": [[11, "ete4.Tree.to_str"]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric"]], "traverse() (tree method)": [[11, "ete4.Tree.traverse"]], "unroot() (tree method)": [[11, "ete4.Tree.unroot"]], "up (tree attribute)": [[11, "ete4.Tree.up"]], "write() (tree method)": [[11, "ete4.Tree.write"]], "treepattern (class in ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.TreePattern"]], "__init__() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.__init__"]], "ete4.treematcher.treematcher": [[12, "module-ete4.treematcher.treematcher"]], "match() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.match"]], "match() (in module ete4.treematcher.treematcher)": [[12, "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