diff --git a/_modules/ete4/gtdb_taxonomy/gtdbquery.html b/_modules/ete4/gtdb_taxonomy/gtdbquery.html new file mode 100644 index 000000000..d4c94accb --- /dev/null +++ b/_modules/ete4/gtdb_taxonomy/gtdbquery.html @@ -0,0 +1,985 @@ + + + + + + + ete4.gtdb_taxonomy.gtdbquery — ETE Toolkit 4.0.0-beta documentation + + + + + + + + + + + + + + + + + + +
+
+
+ + +
+ +

Source code for ete4.gtdb_taxonomy.gtdbquery

+#!/usr/bin/env python3
+
+import sys
+import os
+
+import pickle
+from collections import defaultdict, Counter
+
+from hashlib import md5
+
+import sqlite3
+import math
+import tarfile
+import warnings
+
+from ete4 import ETE_DATA_HOME, update_ete_data
+
+
+__all__ = ["GTDBTaxa", "is_taxadb_up_to_date"]
+
+DB_VERSION = 2
+DEFAULT_GTDBTAXADB = ETE_DATA_HOME + '/gtdbtaxa.sqlite'
+DEFAULT_GTDBTAXADUMP = ETE_DATA_HOME + '/gtdb202dump.tar.gz'
+
+
+def is_taxadb_up_to_date(dbfile=DEFAULT_GTDBTAXADB):
+    """Check if a valid and up-to-date gtdbtaxa.sqlite database exists
+    If dbfile= is not specified, DEFAULT_TAXADB is assumed
+    """
+    db = sqlite3.connect(dbfile)
+    try:
+        r = db.execute('SELECT version FROM stats;')
+        version = r.fetchone()[0]
+    except (sqlite3.OperationalError, ValueError, IndexError, TypeError):
+        version = None
+
+    db.close()
+
+    if version != DB_VERSION:
+        return False
+    return True
+
+
+

+[docs]
+class GTDBTaxa:
+    """
+    Local transparent connector to the GTDB taxonomy database.
+    """
+
+

+[docs]
+    def __init__(self, dbfile=None, taxdump_file=None, memory=False):
+
+        if not dbfile:
+            self.dbfile = DEFAULT_GTDBTAXADB
+        else:
+            self.dbfile = dbfile
+
+        if taxdump_file:
+            self.update_taxonomy_database(taxdump_file)
+
+        if dbfile != DEFAULT_GTDBTAXADB and not os.path.exists(self.dbfile):
+            print('GTDB database not present yet (first time used?)', file=sys.stderr)
+            urlbase = ('https://github.com/etetoolkit/ete-data/raw/main'
+                       '/gtdb_taxonomy/gtdb202')
+            update_ete_data(f'{DEFAULT_GTDBTAXADB}.traverse.pkl', f'{urlbase}/gtdbtaxa.sqlite.traverse.pkl')
+            update_ete_data(f'{DEFAULT_GTDBTAXADUMP}', f'{urlbase}/gtdb202dump.tar.gz')
+
+            self.update_taxonomy_database(taxdump_file=DEFAULT_GTDBTAXADUMP)
+
+        if not os.path.exists(self.dbfile):
+            raise ValueError("Cannot open taxonomy database: %s" % self.dbfile)
+
+        self.db = None
+        self._connect()
+
+        if not is_taxadb_up_to_date(self.dbfile):
+            print('GTDB database format is outdated. Upgrading', file=sys.stderr)
+            self.update_taxonomy_database(taxdump_file)
+
+        if memory:
+            filedb = self.db
+            self.db = sqlite3.connect(':memory:')
+            filedb.backup(self.db)

+
+
+

+[docs]
+    def update_taxonomy_database(self, taxdump_file=None):
+        """Update the GTDB taxonomy database.
+
+        It updates it by downloading and parsing the latest
+        gtdbtaxdump.tar.gz file.
+
+        :param taxdump_file: Alternative location of gtdbtaxdump.tar.gz.
+        """
+        update_db(self.dbfile, targz_file=taxdump_file)

+
+
+    def _connect(self):
+        self.db = sqlite3.connect(self.dbfile)
+
+    def _translate_merged(self, all_taxids):
+        conv_all_taxids = set((list(map(int, all_taxids))))
+        cmd = 'select taxid_old, taxid_new FROM merged WHERE taxid_old IN (%s)' %','.join(map(str, all_taxids))
+
+        result = self.db.execute(cmd)
+        conversion = {}
+        for old, new in result.fetchall():
+            conv_all_taxids.discard(int(old))
+            conv_all_taxids.add(int(new))
+            conversion[int(old)] = int(new)
+        return conv_all_taxids, conversion
+
+
+    # def get_fuzzy_name_translation(self, name, sim=0.9):
+    #     '''
+    #     Given an inexact species name, returns the best match in the NCBI database of taxa names.
+    #     :argument 0.9 sim: Min word similarity to report a match (from 0 to 1).
+    #     :return: taxid, species-name-match, match-score
+    #     '''
+
+
+    #     import sqlite3.dbapi2 as dbapi2
+    #     _db = dbapi2.connect(self.dbfile)
+    #     _db.enable_load_extension(True)
+    #     module_path = os.path.split(os.path.realpath(__file__))[0]
+    #     _db.execute("select load_extension('%s')" % os.path.join(module_path,
+    #                                                              "SQLite-Levenshtein/levenshtein.sqlext"))
+
+    #     print("Trying fuzzy search for %s" % name)
+    #     maxdiffs = math.ceil(len(name) * (1-sim))
+    #     cmd = 'SELECT taxid, spname, LEVENSHTEIN(spname, "%s") AS sim  FROM species WHERE sim<=%s ORDER BY sim LIMIT 1;' % (name, maxdiffs)
+    #     taxid, spname, score = None, None, len(name)
+    #     result = _db.execute(cmd)
+    #     try:
+    #         taxid, spname, score = result.fetchone()
+    #     except TypeError:
+    #         cmd = 'SELECT taxid, spname, LEVENSHTEIN(spname, "%s") AS sim  FROM synonym WHERE sim<=%s ORDER BY sim LIMIT 1;' % (name, maxdiffs)
+    #         result = _db.execute(cmd)
+    #         try:
+    #             taxid, spname, score = result.fetchone()
+    #         except:
+    #             pass
+    #         else:
+    #             taxid = int(taxid)
+    #     else:
+    #         taxid = int(taxid)
+
+    #     norm_score = 1 - (float(score)/len(name))
+    #     if taxid:
+    #         print("FOUND!    %s taxid:%s score:%s (%s)" %(spname, taxid, score, norm_score))
+
+    #     return taxid, spname, norm_score
+
+

+[docs]
+    def get_rank(self, taxids):
+        """Return dictionary converting taxids to their GTDB taxonomy rank."""
+        ids = ','.join('"%s"' % v for v in set(taxids) - {None, ''})
+        result = self.db.execute('SELECT taxid, rank FROM species WHERE taxid IN (%s)' % ids)
+        return {tax: spname for tax, spname in result.fetchall()}

+
+
+

+[docs]
+    def get_lineage_translator(self, taxids):
+        """Given a valid taxid number, return its corresponding lineage track as a
+        hierarchically sorted list of parent taxids.
+        """
+        all_ids = set(taxids)
+        all_ids.discard(None)
+        all_ids.discard("")
+        query = ','.join(['"%s"' %v for v in all_ids])
+        result = self.db.execute('SELECT taxid, track FROM species WHERE taxid IN (%s);' %query)
+        id2lineages = {}
+        for tax, track in result.fetchall():
+            id2lineages[tax] = list(map(int, reversed(track.split(","))))
+
+        return id2lineages

+
+
+

+[docs]
+    def get_name_lineage(self, taxnames):
+        """Given a valid taxname, return its corresponding lineage track as a
+        hierarchically sorted list of parent taxnames.
+        """
+        name_lineages = []
+        name2taxid = self.get_name_translator(taxnames)
+        for key, value in name2taxid.items():
+            lineage = self.get_lineage(value[0])
+            names = self.get_taxid_translator(lineage)
+            name_lineages.append({key:[names[taxid] for taxid in lineage]})
+
+        return name_lineages

+
+
+

+[docs]
+    def get_lineage(self, taxid):
+        """Given a valid taxid number, return its corresponding lineage track as a
+        hierarchically sorted list of parent taxids.
+        """
+        if not taxid:
+            return None
+        taxid = int(taxid)
+        result = self.db.execute('SELECT track FROM species WHERE taxid=%s' %taxid)
+        raw_track = result.fetchone()
+        if not raw_track:
+            #perhaps is an obsolete taxid
+            _, merged_conversion = self._translate_merged([taxid])
+            if taxid in merged_conversion:
+                result = self.db.execute('SELECT track FROM species WHERE taxid=%s' %merged_conversion[taxid])
+                raw_track = result.fetchone()
+            # if not raise error
+            if not raw_track:
+                #raw_track = ["1"]
+                raise ValueError("%s taxid not found" %taxid)
+            else:
+                warnings.warn("taxid %s was translated into %s" %(taxid, merged_conversion[taxid]))
+
+        track = list(map(int, raw_track[0].split(",")))
+        return list(reversed(track))

+
+
+

+[docs]
+    def get_common_names(self, taxids):
+        query = ','.join(['"%s"' %v for v in taxids])
+        cmd = "select taxid, common FROM species WHERE taxid IN (%s);" %query
+        result = self.db.execute(cmd)
+        id2name = {}
+        for tax, common_name in result.fetchall():
+            if common_name:
+                id2name[tax] = common_name
+        return id2name

+
+
+

+[docs]
+    def get_taxid_translator(self, taxids, try_synonyms=True):
+        """Given a list of taxids, returns a dictionary with their corresponding
+        scientific names.
+        """
+
+        all_ids = set(map(int, taxids))
+        all_ids.discard(None)
+        all_ids.discard("")
+        query = ','.join(['"%s"' %v for v in all_ids])
+        cmd = "select taxid, spname FROM species WHERE taxid IN (%s);" %query
+        result = self.db.execute(cmd)
+        id2name = {}
+        for tax, spname in result.fetchall():
+            id2name[tax] = spname
+
+        # any taxid without translation? lets tray in the merged table
+        # if len(all_ids) != len(id2name) and try_synonyms:
+        #     not_found_taxids = all_ids - set(id2name.keys())
+        #     taxids, old2new = self._translate_merged(not_found_taxids)
+        #     new2old = {v: k for k,v in old2new.items()}
+
+        #     if old2new:
+        #         query = ','.join(['"%s"' %v for v in new2old])
+        #         cmd = "select taxid, spname FROM species WHERE taxid IN (%s);" %query
+        #         result = self.db.execute(cmd)
+        #         for tax, spname in result.fetchall():
+        #             id2name[new2old[tax]] = spname
+
+        return id2name

+
+
+

+[docs]
+    def get_name_translator(self, names):
+        """
+        Given a list of taxid scientific names, returns a dictionary translating them into their corresponding taxids.
+        Exact name match is required for translation.
+        """
+
+        name2id = {}
+        #name2realname = {}
+        name2origname = {}
+        for n in names:
+            name2origname[n.lower()] = n
+
+        names = set(name2origname.keys())
+
+        query = ','.join(['"%s"' %n for n in name2origname.keys()])
+        cmd = 'select spname, taxid from species where spname IN (%s)' %query
+        result = self.db.execute('select spname, taxid from species where spname IN (%s)' %query)
+        for sp, taxid in result.fetchall():
+            oname = name2origname[sp.lower()]
+            name2id.setdefault(oname, []).append(taxid)
+            #name2realname[oname] = sp
+        missing =  names - set([n.lower() for n in name2id.keys()])
+        if missing:
+            query = ','.join(['"%s"' %n for n in missing])
+            result = self.db.execute('select spname, taxid from synonym where spname IN (%s)' %query)
+            for sp, taxid in result.fetchall():
+                oname = name2origname[sp.lower()]
+                name2id.setdefault(oname, []).append(taxid)
+                #name2realname[oname] = sp
+        return name2id

+
+
+

+[docs]
+    def translate_to_names(self, taxids):
+        """
+        Given a list of taxid numbers, returns another list with their corresponding scientific names.
+        """
+        id2name = self.get_taxid_translator(taxids)
+        names = []
+        for sp in taxids:
+            names.append(id2name.get(sp, sp))
+        return names

+
+
+
+

+[docs]
+    def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, return_tree=False):
+        """
+        given a parent taxid or scientific species name, returns a list of all its descendants taxids.
+        If intermediate_nodes is set to True, internal nodes will also be dumped.
+        """
+        try:
+            taxid = int(parent)
+        except ValueError:
+            try:
+                taxid = self.get_name_translator([parent])[parent][0]
+            except KeyError:
+                raise ValueError('%s not found!' %parent)
+
+        # checks if taxid is a deprecated one, and converts into the right one.
+        _, conversion = self._translate_merged([taxid]) #try to find taxid in synonyms table
+        if conversion:
+            taxid = conversion[taxid]
+
+        with open(self.dbfile+".traverse.pkl", "rb") as CACHED_TRAVERSE:
+            prepostorder = pickle.load(CACHED_TRAVERSE)
+        descendants = {}
+        found = 0
+        for tid in prepostorder:
+            if tid == taxid:
+                found += 1
+            elif found == 1:
+                descendants[tid] = descendants.get(tid, 0) + 1
+            elif found == 2:
+                break
+
+        if not found:
+            raise ValueError("taxid not found:%s" %taxid)
+        elif found == 1:
+            return [taxid]
+        if rank_limit or collapse_subspecies or return_tree:
+            descendants_spnames = self.get_taxid_translator(list(descendants.keys()))
+            #tree = self.get_topology(list(descendants.keys()), intermediate_nodes=intermediate_nodes, collapse_subspecies=collapse_subspecies, rank_limit=rank_limit)
+            tree = self.get_topology(list(descendants_spnames.values()), intermediate_nodes=intermediate_nodes, collapse_subspecies=collapse_subspecies, rank_limit=rank_limit)
+            if return_tree:
+                return tree
+            elif intermediate_nodes:
+                return [n.name for n in tree.get_descendants()]
+            else:
+                return [n.name for n in tree]
+
+        elif intermediate_nodes:
+            return self.translate_to_names([tid for tid, count in descendants.items()])
+        else:
+            self.translate_to_names([tid for tid, count in descendants.items() if count == 1])
+            return self.translate_to_names([tid for tid, count in descendants.items() if count == 1])

+
+
+

+[docs]
+    def get_topology(self, taxnames, intermediate_nodes=False, rank_limit=None,
+                     collapse_subspecies=False, annotate=True):
+        """Return minimal pruned GTDB taxonomy tree containing all given taxids.
+
+        :param intermediate_nodes: If True, single child nodes
+            representing the complete lineage of leaf nodes are kept.
+            Otherwise, the tree is pruned to contain the first common
+            ancestor of each group.
+        :param rank_limit: If valid NCBI rank name is provided, the
+            tree is pruned at that given level. For instance, use
+            rank="species" to get rid of sub-species or strain leaf
+            nodes.
+        :param collapse_subspecies: If True, any item under the
+            species rank will be collapsed into the species upper
+            node.
+        """
+        from .. import PhyloTree
+        #taxids, merged_conversion = self._translate_merged(taxids)
+        tax2id = self.get_name_translator(taxnames) #{'f__Korarchaeaceae': [2174], 'o__Peptococcales': [205487], 'p__Huberarchaeota': [610]}
+        taxids = [i[0] for i in tax2id.values()]
+
+        if len(taxids) == 1:
+            root_taxid = int(list(taxids)[0])
+            with open(self.dbfile+".traverse.pkl", "rb") as CACHED_TRAVERSE:
+                prepostorder = pickle.load(CACHED_TRAVERSE)
+            descendants = {}
+            found = 0
+            nodes = {}
+            hit = 0
+            visited = set()
+            start = prepostorder.index(root_taxid)
+            try:
+            	end = prepostorder.index(root_taxid, start+1)
+            	subtree = prepostorder[start:end+1]
+            except ValueError:
+                # If root taxid is not found in postorder, must be a tip node
+            	subtree = [root_taxid]
+            leaves = set([v for v, count in Counter(subtree).items() if count == 1])
+            tax2name = self.get_taxid_translator(list(subtree))
+            name2tax ={spname:taxid for taxid,spname in tax2name.items()}
+            nodes[root_taxid] = PhyloTree(name=root_taxid)
+            current_parent = nodes[root_taxid]
+            for tid in subtree:
+                if tid in visited:
+                    current_parent = nodes[tid].up
+                else:
+                    visited.add(tid)
+                    nodes[tid] = PhyloTree(name=tax2name.get(tid, ''))
+                    current_parent.add_child(nodes[tid])
+                    if tid not in leaves:
+                        current_parent = nodes[tid]
+            root = nodes[root_taxid]
+        else:
+            taxids = set(map(int, taxids))
+            sp2track = {}
+            elem2node = {}
+            id2lineage = self.get_lineage_translator(taxids)
+            all_taxids = set()
+            for lineage in id2lineage.values():
+                all_taxids.update(lineage)
+            id2rank = self.get_rank(all_taxids)
+
+            tax2name = self.get_taxid_translator(taxids)
+            all_taxid_codes = set([_tax for _lin in list(id2lineage.values()) for _tax in _lin])
+            extra_tax2name = self.get_taxid_translator(list(all_taxid_codes - set(tax2name.keys())))
+            tax2name.update(extra_tax2name)
+            name2tax ={spname:taxid for taxid,spname in tax2name.items()}
+
+            for sp in taxids:
+                track = []
+                lineage = id2lineage[sp]
+
+                for elem in lineage:
+                    spanme = tax2name[elem]
+                    if elem not in elem2node:
+                        node = elem2node.setdefault(elem, PhyloTree())
+                        node.name = str(tax2name[elem])
+                        node.taxid = str(tax2name[elem])
+                        node.add_prop("rank", str(id2rank.get(int(elem), "no rank")))
+                    else:
+                        node = elem2node[elem]
+                    track.append(node)
+                sp2track[sp] = track
+            # generate parent child relationships
+            for sp, track in sp2track.items():
+                parent = None
+                for elem in track:
+                    if parent and elem not in parent.children:
+                        parent.add_child(elem)
+                    if rank_limit and elem.props.get('rank') == rank_limit:
+                        break
+                    parent = elem
+            root = elem2node[1]
+        #remove onechild-nodes
+
+        if not intermediate_nodes:
+            for n in root.descendants():
+                if len(n.children) == 1 and int(name2tax.get(n.name, n.name)) not in taxids:
+                    n.delete(prevent_nondicotomic=False)
+
+        if len(root.children) == 1:
+            tree = root.children[0].detach()
+        else:
+            tree = root
+
+        if collapse_subspecies:
+            to_detach = []
+            for node in tree.traverse():
+                if node.props.get('rank') == 'species':
+                    to_detach.extend(node.children)
+            for n in to_detach:
+                n.detach()
+
+        if annotate:
+            self.annotate_tree(tree)
+
+        return tree

+
+
+

+[docs]
+    def annotate_tree(self, t, taxid_attr='name',
+                      tax2name=None, tax2track=None, tax2rank=None):
+        """Annotate a tree containing taxids as leaf names.
+
+        It annotates by adding the properties 'taxid', 'sci_name',
+        'lineage', 'named_lineage' and 'rank'.
+
+        :param t: Tree to annotate.
+        :param taxid_attr: Node attribute (property) containing the
+            taxid number associated to each node (i.e. species in
+            PhyloTree instances).
+        :param tax2name, tax2track, tax2rank: Pre-calculated
+            dictionaries with translations from taxid number to names,
+            track lineages and ranks.
+        """
+        taxids = set()
+        if taxid_attr == "taxid":
+            for n in t.traverse():
+                if taxid_attr in n.props:
+                    taxids.add(n.props[taxid_attr])
+        else:
+            for n in t.traverse():
+                try:
+                    # translate gtdb name -> id
+                    taxaname = n.props.get(taxid_attr)
+                    tid = self.get_name_translator([taxaname])[taxaname][0]
+                    taxids.add(tid)
+                except (KeyError, ValueError, AttributeError):
+                    pass
+        merged_conversion = {}
+
+        taxids, merged_conversion = self._translate_merged(taxids)
+
+        if not tax2name or taxids - set(map(int, list(tax2name.keys()))):
+            tax2name = self.get_taxid_translator(taxids)
+        if not tax2track or taxids - set(map(int, list(tax2track.keys()))):
+            tax2track = self.get_lineage_translator(taxids)
+
+        all_taxid_codes = set([_tax for _lin in list(tax2track.values()) for _tax in _lin])
+        extra_tax2name = self.get_taxid_translator(list(all_taxid_codes - set(tax2name.keys())))
+        tax2name.update(extra_tax2name)
+
+        tax2common_name = self.get_common_names(tax2name.keys())
+
+        if not tax2rank:
+            tax2rank = self.get_rank(list(tax2name.keys()))
+
+        name2tax ={spname:taxid for taxid,spname in tax2name.items()}
+        n2leaves = t.get_cached_content()
+
+        for node in t.traverse('postorder'):
+            node_taxid = node.props.get(taxid_attr)
+
+            node.add_prop('taxid', node_taxid)
+
+            if node_taxid:
+                tmp_taxid = self.get_name_translator([node_taxid]).get(node_taxid, [None])[0]
+
+                if node_taxid in merged_conversion:
+                    node_taxid = merged_conversion[node_taxid]
+
+                rank = tax2rank.get(tmp_taxid, 'Unknown')
+                if rank != 'subspecies':
+                    sci_name = tax2name.get(tmp_taxid, '')
+                else:
+                    # For subspecies, gtdb taxid (like 'RS_GCF_0062.1') is not informative. Better use the species one.
+                    track = tax2track[tmp_taxid]  # like ['root', 'd__Bacteria', ..., 's__Moorella', 'RS_GCF_0062.1']
+                    sci_name = tax2name.get(track[-2], '')
+
+                node.add_props(sci_name = sci_name,
+                               common_name = tax2common_name.get(node_taxid, ''),
+                               lineage = tax2track.get(tmp_taxid, []),
+                               rank = tax2rank.get(tmp_taxid, 'Unknown'),
+                               named_lineage = [tax2name.get(tax, str(tax)) for tax in tax2track.get(tmp_taxid, [])])
+            elif node.is_leaf:
+                node.add_props(sci_name = node.props.get(taxid_attr, 'NA'),
+                               common_name = '',
+                               lineage = [],
+                               rank = 'Unknown',
+                               named_lineage = [])
+            else:
+                lineage = self._common_lineage([lf.props.get('lineage') for lf in n2leaves[node]])
+                if lineage[-1]:
+                    ancestor = self.get_taxid_translator([lineage[-1]])[lineage[-1]]
+                else:
+                    ancestor = None
+                node.add_props(sci_name = tax2name.get(ancestor, str(ancestor)),
+                               common_name = tax2common_name.get(lineage[-1], ''),
+                               taxid = ancestor,
+                               lineage = lineage,
+                               rank = tax2rank.get(lineage[-1], 'Unknown'),
+                               named_lineage = [tax2name.get(tax, str(tax)) for tax in lineage])
+
+        return tax2name, tax2track, tax2rank

+
+
+    def _common_lineage(self, vectors):
+        occurrence = defaultdict(int)
+        pos = defaultdict(set)
+        for v in vectors:
+            for i, taxid in enumerate(v):
+                occurrence[taxid] += 1
+                pos[taxid].add(i)
+
+        common = [taxid for taxid, ocu in occurrence.items() if ocu == len(vectors)]
+        if not common:
+            return [""]
+        else:
+            sorted_lineage = sorted(common, key=lambda x: min(pos[x]))
+            return sorted_lineage
+
+        # OLD APPROACH:
+
+        # visited = defaultdict(int)
+        # for index, name in [(ei, e) for v in vectors for ei, e in enumerate(v)]:
+        #     visited[(name, index)] += 1
+
+        # def _sort(a, b):
+        #     if a[1] > b[1]:
+        #         return 1
+        #     elif a[1] < b[1]:
+        #         return -1
+        #     else:
+        #         if a[0][1] > b[0][1]:
+        #             return 1
+        #         elif a[0][1] < b[0][1]:
+        #             return -1
+        #     return 0
+
+        # matches = sorted(visited.items(), _sort)
+
+        # if matches:
+        #     best_match = matches[-1]
+        # else:
+        #     return "", set()
+
+        # if best_match[1] != len(vectors):
+        #     return "", set()
+        # else:
+        #     return best_match[0][0], [m[0][0] for m in matches if m[1] == len(vectors)]
+
+
+

+[docs]
+    def get_broken_branches(self, t, taxa_lineages, n2content=None):
+        """Returns a list of GTDB lineage names that are not monophyletic in the
+        provided tree, as well as the list of affected branches and their size.
+        CURRENTLY EXPERIMENTAL
+        """
+        if not n2content:
+            n2content = t.get_cached_content()
+
+        tax2node = defaultdict(set)
+
+        unknown = set()
+        for leaf in t.iter_leaves():
+            if leaf.sci_name.lower() != "unknown":
+                lineage = taxa_lineages[leaf.taxid]
+                for index, tax in enumerate(lineage):
+                    tax2node[tax].add(leaf)
+            else:
+                unknown.add(leaf)
+
+        broken_branches = defaultdict(set)
+        broken_clades = set()
+        for tax, leaves in tax2node.items():
+            if len(leaves) > 1:
+                common = t.get_common_ancestor(leaves)
+            else:
+                common = list(leaves)[0]
+            if (leaves ^ set(n2content[common])) - unknown:
+                broken_branches[common].add(tax)
+                broken_clades.add(tax)
+
+        broken_clade_sizes = [len(tax2node[tax]) for tax in broken_clades]
+        return broken_branches, broken_clades, broken_clade_sizes

+

+
+
+
+    # TODO: See why this code is commented out and comment it properly or remove it.
+    #
+    # def annotate_tree_with_taxa(self, t, name2taxa_file, tax2name=None, tax2track=None, attr_name="name"):
+    #     if name2taxa_file:
+    #         names2taxid = dict([map(strip, line.split("\t"))
+    #                             for line in open(name2taxa_file)])
+    #     else:
+    #         names2taxid = dict([(n.name, getattr(n, attr_name)) for n in t.iter_leaves()])
+
+    #     not_found = 0
+    #     for n in t.iter_leaves():
+    #         n.add_features(taxid=names2taxid.get(n.name, 0))
+    #         n.add_features(species=n.taxid)
+    #         if n.taxid == 0:
+    #             not_found += 1
+    #     if not_found:
+    #         print >>sys.stderr, "WARNING: %s nodes where not found within NCBI taxonomy!!" %not_found
+
+    #     return self.annotate_tree(t, tax2name, tax2track, attr_name="taxid")
+
+
+def load_gtdb_tree_from_dump(tar):
+    from .. import Tree
+    # Download: gtdbdump/gtdbr202dump.tar.z
+    parent2child = {}
+    name2node = {}
+    node2taxname = {}
+    synonyms = set()
+    name2rank = {}
+    node2common = {}
+    print("Loading node names...")
+    unique_nocase_synonyms = set()
+    for line in tar.extractfile("names.dmp"):
+        line = str(line.decode())
+        fields =  [_f.strip() for _f in line.split("|")]
+        nodename = fields[0]
+        name_type = fields[3].lower()
+        taxname = fields[1]
+
+        # Clean up tax names so we make sure the don't include quotes. See https://github.com/etetoolkit/ete/issues/469
+        taxname = taxname.rstrip('"').lstrip('"')
+
+        if name_type == "scientific name":
+            node2taxname[nodename] = taxname
+        if name_type == "genbank common name":
+            node2common[nodename] = taxname
+        elif name_type in set(["synonym", "equivalent name", "genbank equivalent name",
+                               "anamorph", "genbank synonym", "genbank anamorph", "teleomorph"]):
+
+            # Keep track synonyms, but ignore duplicate case-insensitive names. See https://github.com/etetoolkit/ete/issues/469
+            synonym_key = (nodename, taxname.lower())
+            if synonym_key not in unique_nocase_synonyms:
+                unique_nocase_synonyms.add(synonym_key)
+                synonyms.add((nodename, taxname))
+
+    print(len(node2taxname), "names loaded.")
+    print(len(synonyms), "synonyms loaded.")
+
+    print("Loading nodes...")
+    for line in tar.extractfile("nodes.dmp"):
+        line = str(line.decode())
+        fields =  line.split("|")
+        nodename = fields[0].strip()
+        parentname = fields[1].strip()
+        try:
+            n = Tree()
+        except:
+            from .. import Tree
+            n = Tree()
+        n.name = nodename
+        #n.taxname = node2taxname[nodename]
+        n.add_prop('taxname', node2taxname[nodename])
+        if nodename in node2common:
+            n.add_prop('common_name', node2taxname[nodename])
+        n.add_prop('rank', fields[2].strip())
+        parent2child[nodename] = parentname
+        name2node[nodename] = n
+    print(len(name2node), "nodes loaded.")
+
+    print("Linking nodes...")
+    for node in name2node:
+       if node == "1":
+           t = name2node[node]
+       else:
+           parent = parent2child[node]
+           parent_node = name2node[parent]
+           parent_node.add_child(name2node[node])
+    print("Tree is loaded.")
+    return t, synonyms
+
+def generate_table(t):
+    OUT = open("taxa.tab", "w")
+    for j, n in enumerate(t.traverse()):
+        if j%1000 == 0:
+            print("\r",j,"generating entries...", end=' ')
+        temp_node = n
+        track = []
+        while temp_node:
+            track.append(temp_node.name)
+            temp_node = temp_node.up
+        if n.up:
+            print('\t'.join([n.name, n.up.name, n.props.get('taxname'), n.props.get("common_name", ''), n.props.get("rank"), ','.join(track)]), file=OUT)
+        else:
+            print('\t'.join([n.name, "", n.props.get('taxname'), n.props.get("common_name", ''), n.props.get("rank"), ','.join(track)]), file=OUT)
+    OUT.close()
+
+
+def update_db(dbfile, targz_file=None):
+    basepath = os.path.split(dbfile)[0]
+    if basepath and not os.path.exists(basepath):
+        os.mkdir(basepath)
+
+    try:
+        tar = tarfile.open(targz_file, 'r')
+    except:
+        raise ValueError("Please provide taxa dump tar.gz file")
+
+    t, synonyms = load_gtdb_tree_from_dump(tar)
+
+    prepostorder = [int(node.name) for post, node in t.iter_prepostorder()]
+
+    with open(dbfile+'.traverse.pkl', 'wb') as fout:
+        pickle.dump(prepostorder, fout, 2)
+
+    print("Updating database: %s ..." %dbfile)
+    generate_table(t)
+
+    upload_data(dbfile)
+
+    os.system("rm taxa.tab")
+
+def upload_data(dbfile):
+    print()
+    print('Uploading to', dbfile)
+    basepath = os.path.split(dbfile)[0]
+    if basepath and not os.path.exists(basepath):
+        os.mkdir(basepath)
+
+    db = sqlite3.connect(dbfile)
+
+    create_cmd = """
+    DROP TABLE IF EXISTS stats;
+    DROP TABLE IF EXISTS species;
+    DROP TABLE IF EXISTS synonym;
+    DROP TABLE IF EXISTS merged;
+    CREATE TABLE stats (version INT PRIMARY KEY);
+    CREATE TABLE species (taxid INT PRIMARY KEY, parent INT, spname VARCHAR(50) COLLATE NOCASE, common VARCHAR(50) COLLATE NOCASE, rank VARCHAR(50), track TEXT);
+    CREATE TABLE synonym (taxid INT,spname VARCHAR(50) COLLATE NOCASE, PRIMARY KEY (spname, taxid));
+    CREATE TABLE merged (taxid_old INT, taxid_new INT);
+    CREATE INDEX spname1 ON species (spname COLLATE NOCASE);
+    CREATE INDEX spname2 ON synonym (spname COLLATE NOCASE);
+    """
+    for cmd in create_cmd.split(';'):
+        db.execute(cmd)
+    print()
+
+    db.execute("INSERT INTO stats (version) VALUES (%d);" %DB_VERSION)
+    db.commit()
+
+    # for i, line in enumerate(open("syn.tab")):
+    #     if i%5000 == 0 :
+    #         print('\rInserting synonyms:     % 6d' %i, end=' ', file=sys.stderr)
+    #         sys.stderr.flush()
+    #     taxid, spname = line.strip('\n').split('\t')
+    #     db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))
+    # print()
+    # db.commit()
+    # for i, line in enumerate(open("merged.tab")):
+    #     if i%5000 == 0 :
+    #         print('\rInserting taxid merges: % 6d' %i, end=' ', file=sys.stderr)
+    #         sys.stderr.flush()
+    #     taxid_old, taxid_new = line.strip('\n').split('\t')
+    #     db.execute("INSERT INTO merged (taxid_old, taxid_new) VALUES (?, ?);", (taxid_old, taxid_new))
+    # print()
+    # db.commit()
+
+    with open('taxa.tab') as f_taxa:
+        for i, line in enumerate(f_taxa):
+            if i % 5000 == 0:
+                print('\rInserting taxids: %8d' % i, end=' ', file=sys.stderr)
+                sys.stderr.flush()
+            taxid, parentid, spname, common, rank, lineage = line.strip('\n').split('\t')
+            db.execute(('INSERT INTO species          (taxid, parent, spname, common, rank, track) '
+                        'VALUES (?, ?, ?, ?, ?, ?)'), (taxid, parentid, spname, common, rank, lineage))
+    print()
+    db.commit()
+
+if __name__ == "__main__":
+    #from .. import PhyloTree
+    gtdb = GTDBTaxa()
+    gtdb.update_taxonomy_database(DEFAULT_GTDBTAXADUMP)
+
+    descendants = gtdb.get_descendant_taxa('c__Thorarchaeia', collapse_subspecies=True, return_tree=True)
+    print(descendants.write(properties=None))
+    print(descendants.get_ascii(properties=['sci_name', 'taxid','rank']))
+    tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae", "s__Korarchaeum"], intermediate_nodes=True, collapse_subspecies=True, annotate=True)
+    print(tree.get_ascii(properties=["taxid",  "sci_name", "rank"]))
+
+    tree = PhyloTree('((c__Thorarchaeia, c__Lokiarchaeia_A), s__Caballeronia udeis);', sp_naming_function=lambda name: name)
+    tax2name, tax2track, tax2rank = gtdb.annotate_tree(tree, taxid_attr="name")
+    print(tree.get_ascii(properties=["taxid","name", "sci_name", "rank"]))
+
+    print(gtdb.get_name_lineage(['RS_GCF_006228565.1','GB_GCA_001515945.1']))
+
+ +
+ +
+
+ +
+
+
+ ©2008 - 2023, The ETE Toolkit Team. + + | + Powered by Sphinx 7.2.6 + & Alabaster 0.7.13 + +
+ + + + + + \ No newline at end of file diff --git a/_modules/ete4/ncbi_taxonomy/ncbiquery.html b/_modules/ete4/ncbi_taxonomy/ncbiquery.html index efb6ec5ff..9efbdc345 100644 --- a/_modules/ete4/ncbi_taxonomy/ncbiquery.html +++ b/_modules/ete4/ncbi_taxonomy/ncbiquery.html @@ -55,8 +55,6 @@

Source code for ete4.ncbi_taxonomy.ncbiquery

DEFAULT_TAXDUMP = ETE_DATA_HOME + '/taxdump.tar.gz'
 
 
-

-[docs]
 def is_taxadb_up_to_date(dbfile=DEFAULT_TAXADB):
     """Return True if a valid and up-to-date taxa.sqlite database exists.
 
@@ -71,19 +69,18 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
db.close()
 
-    return version == DB_VERSION

-
+    return version == DB_VERSION
 
 
 

-[docs]
+[docs]
 class NCBITaxa:
     """
     A local transparent connector to the NCBI taxonomy database.
     """
 
 

-[docs]
+[docs]
     def __init__(self, dbfile=None, taxdump_file=None,
                  memory=False, update=True):
         """Open and keep a connection to the NCBI taxonomy database.
@@ -120,7 +117,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def update_taxonomy_database(self, taxdump_file=None):
         """Update the ncbi taxonomy database.
 
@@ -154,7 +151,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
return conv_all_taxids, conversion
 
 

-[docs]
+[docs]
     def get_fuzzy_name_translation(self, name, sim=0.9):
         """Return taxid, species name and match score from the NCBI database.
 
@@ -203,7 +200,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_rank(self, taxids):
         """Return dict with NCBI taxonomy ranks for each list of taxids."""
         all_ids = set(taxids)
@@ -222,7 +219,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_lineage_translator(self, taxids):
         """Return dict with lineage tracks corresponding to the given taxids.
 
@@ -244,7 +241,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_lineage(self, taxid):
         """Return lineage track corresponding to the given taxid.
 
@@ -276,7 +273,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_common_names(self, taxids):
         query = ','.join('"%s"' % v for v in taxids)
         cmd = 'SELECT taxid, common FROM species WHERE taxid IN (%s);' % query
@@ -291,7 +288,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_taxid_translator(self, taxids, try_synonyms=True):
         """Return dict with the scientific names corresponding to the taxids."""
         all_ids = set(map(int, taxids))
@@ -323,7 +320,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_name_translator(self, names):
         """Return dict with taxids corresponding to the given scientific names.
 
@@ -357,7 +354,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def translate_to_names(self, taxids):
         """Return list of scientific names corresponding to taxids."""
         id2name = self.get_taxid_translator(taxids)
@@ -368,7 +365,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_descendant_taxa(self, parent, intermediate_nodes=False,
                             rank_limit=None, collapse_subspecies=False,
                             return_tree=False):
@@ -424,7 +421,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def get_topology(self, taxids, intermediate_nodes=False, rank_limit=None,
                      collapse_subspecies=False, annotate=True):
         """Return the minimal pruned NCBI taxonomy tree containing taxids.
@@ -532,7 +529,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
-[docs]
+[docs]
     def annotate_tree(self, t, taxid_attr="name", tax2name=None,
                       tax2track=None, tax2rank=None):
         """Annotate a tree containing taxids as leaf names.
@@ -625,7 +622,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
return sorted_lineage
 
 

-[docs]
+[docs]
     def get_broken_branches(self, t, taxa_lineages, n2content=None):
         """Returns a list of NCBI lineage names that are not monophyletic in the
         provided tree, as well as the list of affected branches and their size.
diff --git a/_modules/index.html b/_modules/index.html
index 8734c95de..f7ad41bd3 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -35,6 +35,7 @@ 
All modules for which code is available

 
  • ete4.core.operations
    • 
 
  • ete4.core.seqgroup
    • 
 
  • ete4.core.tree
    • 
+
  • ete4.gtdb_taxonomy.gtdbquery
    • 
 
  • ete4.ncbi_taxonomy.ncbiquery
    • 
 
  • ete4.parser.newick
    • 
 
  • ete4.parser.nexus
    • 
diff --git a/_sources/reference/index.rst.txt b/_sources/reference/index.rst.txt
index 4d95c594b..8e94bd376 100644
--- a/_sources/reference/index.rst.txt
+++ b/_sources/reference/index.rst.txt
@@ -10,6 +10,6 @@ Reference Guide
    reference_phylo
    reference_clustering
    reference_seqgroup
-   reference_ncbi
+   reference_taxonomy
    reference_smartview
    reference_treeview
diff --git a/_sources/reference/reference_ncbi.rst.txt b/_sources/reference/reference_ncbi.rst.txt
deleted file mode 100644
index e79cc6d92..000000000
--- a/_sources/reference/reference_ncbi.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-NCBITaxa
-========
-
-.. automodule:: ete4.ncbi_taxonomy.ncbiquery
-   :members:
-   :undoc-members:
-   :special-members: __init__
diff --git a/_sources/reference/reference_phylo.rst.txt b/_sources/reference/reference_phylo.rst.txt
index cc285cef8..3f565b6c4 100644
--- a/_sources/reference/reference_phylo.rst.txt
+++ b/_sources/reference/reference_phylo.rst.txt
@@ -1,12 +1,19 @@
 Phylogenetic trees
 ==================
 
+PhyloTree
+---------
+
 .. autoclass:: ete4.PhyloTree
    :members:
    :undoc-members:
    :show-inheritance:
    :special-members: __init__
 
+
+EvolEvent
+---------
+
 .. autoclass:: ete4.phylo.EvolEvent
    :members:
    :undoc-members:
diff --git a/_sources/reference/reference_taxonomy.rst.txt b/_sources/reference/reference_taxonomy.rst.txt
new file mode 100644
index 000000000..58b5d03e0
--- /dev/null
+++ b/_sources/reference/reference_taxonomy.rst.txt
@@ -0,0 +1,19 @@
+Taxonomy databases
+==================
+
+NCBITaxa
+--------
+
+.. autoclass:: ete4.NCBITaxa
+   :members:
+   :undoc-members:
+   :special-members: __init__
+
+
+GTDBTaxa
+--------
+
+.. autoclass:: ete4.GTDBTaxa
+   :members:
+   :undoc-members:
+   :special-members: __init__
diff --git a/_sources/tutorial/index.rst.txt b/_sources/tutorial/index.rst.txt
index a7a6ea1bf..b95647d7f 100644
--- a/_sources/tutorial/index.rst.txt
+++ b/_sources/tutorial/index.rst.txt
@@ -9,3 +9,4 @@ Contents:
    tutorial_trees
    tutorial_phylogeny
    tutorial_drawing
+   tutorial_taxonomy
diff --git a/_sources/tutorial/tutorial_taxonomy.rst.txt b/_sources/tutorial/tutorial_taxonomy.rst.txt
index ddba7256a..eda99887e 100644
--- a/_sources/tutorial/tutorial_taxonomy.rst.txt
+++ b/_sources/tutorial/tutorial_taxonomy.rst.txt
@@ -1,60 +1,74 @@
 .. currentmodule:: ete4
 
-Connecting with Taxonomy Databases
+Taxonomy databases
 ==================
 
 .. contents::
 
 Overview
 --------
-ETE4 contains *ncbi_taxonomy* and *gtdb_taxonomy* modules which provide 
-utilities to efficiently query a local copy of the NCBI or GTDB taxonomy 
-databases. The class ``NCBITaxa`` and ``GTDBTaxa`` offer methods to convert 
-from taxid to names (and vice versa), to fetch pruned topologies connecting 
-a given set of species, or to download rank, names and lineage track information.
 
-It is also fully integrated with PhyloTree instances through the 
-``PhyloNode.annotate_ncbi_taxa()`` and ``PhyloNode.annotate_gtdb_taxa()``method.
+ETE4 contains the *ncbi_taxonomy* and *gtdb_taxonomy* modules which
+provide utilities to efficiently query a local copy of the NCBI or
+GTDB taxonomy databases. The classes :class:`NCBITaxa` and
+:class:`GTDBTaxa` offer methods to convert from taxid to names (and
+vice versa), to fetch pruned topologies connecting a given set of
+species, or to download rank, names and lineage track information.
+
+It is also fully integrated with :class:`PhyloTree` instances through
+the :func:`~PhyloTree.annotate_ncbi_taxa` and
+:func:`~PhyloTree.annotate_gtdb_taxa` methods.
+
 
 Differences between NCBI and GTDB taxonomies in ETE4
 ----------------------------------------------------
 
-The NCBI taxonomy database is a comprehensive resource for organism names and 
-classifications.It is updated daily and offers multiple access points including a web 
-portal, an FTP server. The database releases its data in a package called "taxdump.tar.gz" which 
-contains several .dmp files. 
+The NCBI taxonomy database is a comprehensive resource for organism
+names and classifications.It is updated daily and offers multiple
+access points including a web portal, an FTP server. The database
+releases its data in a package called "taxdump.tar.gz" which contains
+several .dmp files.
 
-Taxon in NCBI taxonomyis usually a numeric identifier, commonly representing 
-taxa ("TaxID"), but it can also signify other entities like genetic codes or citations, such as 
-9606 represents Homo Sapiens. 
+Taxon in NCBI taxonomyis usually a numeric identifier, commonly
+representing taxa ("TaxID"), but it can also signify other entities
+like genetic codes or citations, such as 9606 represents Homo Sapiens.
 
-On the other hand, GTDB taxonomy is distributed as simple text files, uses a genome-based 
-approach for classification, and the identifiers are usually specific to genomes rather 
-than taxa. 
+On the other hand, GTDB taxonomy is distributed as simple text files,
+uses a genome-based approach for classification, and the identifiers
+are usually specific to genomes rather than taxa.
 
-Since ETE Toolkit version 3, ete3 parses taxdump file to local sqlite database to fullfill the 
-methods in ncbi_taxonomy module. We applied the same strategy to GTDBTaxa. While the original GTDB 
-taxonomy data differs from NCBI taxonomy files, a conversion step is essential for integration. 
+Since ETE Toolkit version 3, ETE parses taxdump file and stores it in
+a local sqlite database to fullfill the methods in ncbi_taxonomy
+module. We applied the same strategy to GTDBTaxa. While the original
+GTDB taxonomy data differs from NCBI taxonomy files, a conversion step
+is essential for integration.
+
+To integrate GTDB into the ETE Toolkit v4, a conversion process is
+necessary. A third-party script
+(https://github.com/nick-youngblut/gtdb_to_taxdump) is employed to
+convert the GTDB taxonomy to the NCBI-like taxdump format. We already
+preprared GTDB taxonomy dump file from different releases version and
+store in
+https://github.com/etetoolkit/ete-data/tree/main/gtdb_taxonomy.
 
-To integrate GTDB into the ETE Toolkit v4, a conversion process was necessary. A third-party script
-(https://github.com/nick-youngblut/gtdb_to_taxdump) was employed to convert the GTDB taxonomy to the 
-NCBI-like taxdump format. We already preprared GTDB taxonomy dump file from different releases version 
-and store in https://github.com/etetoolkit/ete-data/tree/main/gtdb_taxonomy.
 
 Setting up local copies of the NCBI and GTDB taxonomy databases
--------------------------------------------------------------
-The first time you attempt to use NCBITaxa or GTDBTaxa, ETE will detect that your local 
-database is empty and it will attempt to download the latest taxonomy database(NCBI ~600MB;GTDB ~72MB) and will 
-store a parsed version of it in your home directory: ~/.local/share/ete/. 
-All future imports of NCBITaxa or GTDBTaxa will detect the local database and will 
-skip this step.
+---------------------------------------------------------------
+
+The first time you attempt to use NCBITaxa or GTDBTaxa, ETE will
+detect that your local database is empty and will attempt to download
+the latest taxonomy database (NCBI ~600MB, GTDB ~72MB) and will store
+a parsed version of it in `~/.local/share/ete/` by default. All future
+imports of NCBITaxa or GTDBTaxa will detect the local database and
+will skip this step.
 
 Example::
+
   # Load NCBI module
   from ete4 import NCBITaxa
   ncbi = NCBITaxa()
   ncbi.update_taxonomy_database()
-  
+
   # Load GTDB module
   from ete4 import GTDBTaxa
   gtdb = GTDBTaxa()
@@ -66,279 +80,280 @@ Example::
 
   # latest release updated in https://github.com/dengzq1234/ete-data/tree/main/gtdb_taxonomy
   gtdb.update_taxonomy_database()
-  # or 
-  gtdb.update_taxonomy_database("gtdbdump.tar.gz") 
+  # or
+  gtdb.update_taxonomy_database("gtdbdump.tar.gz")
 
   # update with custom release 202
   gtdb.update_taxonomy_database('gtdb202dump.tar.gz')
 
+
 Getting taxid information
 -------------------------
 
 NCBI taxonomy
 ~~~~~~~~~~~~~
-you can fetch species names, ranks and linage track information for your taxids using the following 
-methods:
 
-- NCBITaxa.get_rank()
-- NCBITaxa.get_lineage()
-- NCBITaxa.get_taxid_translator()
-- NCBITaxa.get_name_translator()
-- NCBITaxa.translate_to_names()
-The so called get-translator-functions will return a dictionary converting between taxids and species names. 
-Either species or linage names/taxids are accepted as input.
+You can fetch species names, ranks and linage track information for
+your taxids using the following methods:
+
+.. autosummary::
+
+   NCBITaxa.get_rank
+   NCBITaxa.get_lineage
+   NCBITaxa.get_taxid_translator
+   NCBITaxa.get_name_translator
+   NCBITaxa.translate_to_names
+
+The so called get-translator functions will return a dictionary
+converting between taxids and species names. Either species or linage
+names/taxids are accepted as input.
 
 Example::
-    from ete4 import NCBITaxa
-    ncbi = NCBITaxa()
-    taxid2name = ncbi.get_taxid_translator([9606, 9443])
-    print(taxid2name)
-    # {9443: 'Primates', 9606: 'Homo sapiens'}
 
-    name2taxid = ncbi.get_name_translator(['Homo sapiens', 'primates'])
-    print(name2taxid)
-    # {'Homo sapiens': [9606], 'primates': [9443]}
+  from ete4 import NCBITaxa
+  ncbi = NCBITaxa()
+  taxid2name = ncbi.get_taxid_translator([9606, 9443])
+  print(taxid2name)
+  # {9443: 'Primates', 9606: 'Homo sapiens'}
 
-    # when the same name points to several taxa, all taxids are returned
-    name2taxid = ncbi.get_name_translator(['Bacteria'])
-    print(name2taxid)
-    # {'Bacteria': [2, 629395]}
+  name2taxid = ncbi.get_name_translator(['Homo sapiens', 'primates'])
+  print(name2taxid)
+  # {'Homo sapiens': [9606], 'primates': [9443]}
 
-Other functions allow to extract further information using taxid numbers as a query.
+  # when the same name points to several taxa, all taxids are returned
+  name2taxid = ncbi.get_name_translator(['Bacteria'])
+  print(name2taxid)
+  # {'Bacteria': [2, 629395]}
+
+Other functions allow to extract further information using taxid
+numbers as a query.
 
 Example::
-    from ete4 import NCBITaxa
-    ncbi = NCBITaxa()
 
-    print(ncbi.get_rank([9606, 9443]))
-    # {9443: u'order', 9606: u'species'}
+  from ete4 import NCBITaxa
+  ncbi = NCBITaxa()
 
-    print(ncbi.get_lineage(9606))
-    # [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
-    # 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
-    # 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
-    # 9606]
+  print(ncbi.get_rank([9606, 9443]))
+  # {9443: 'order', 9606: 'species'}
 
-Combine combine all at once:
+  print(ncbi.get_lineage(9606))
+  # [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
+  # 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
+  # 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
+  # 9606]
 
-Example::
-    from ete4 import NCBITaxa
-    ncbi = NCBITaxa()
+Example combining all at once::
+
+  from ete4 import NCBITaxa
+  ncbi = NCBITaxa()
 
-    lineage = ncbi.get_lineage(9606)
-    print(lineage)
+  lineage = ncbi.get_lineage(9606)
+  print(lineage)
 
-    # [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
-    # 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
-    # 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
-    # 9606]
+  # [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
+  # 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
+  # 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
+  # 9606]
 
-    names = ncbi.get_taxid_translator(lineage)
-    print([names[taxid] for taxid in lineage])
+  names = ncbi.get_taxid_translator(lineage)
+  print([names[taxid] for taxid in lineage])
 
-    # [u'root', u'cellular organisms', u'Eukaryota', u'Opisthokonta', u'Metazoa',
-    # u'Eumetazoa', u'Bilateria', u'Deuterostomia', u'Chordata', u'Craniata',
-    # u'Vertebrata', u'Gnathostomata', u'Teleostomi', u'Euteleostomi',
-    # u'Sarcopterygii', u'Dipnotetrapodomorpha', u'Tetrapoda', u'Amniota',
-    # u'Mammalia', u'Theria', u'Eutheria', u'Boreoeutheria', u'Euarchontoglires',
-    # u'Primates', u'Haplorrhini', u'Simiiformes', u'Catarrhini', u'Hominoidea',
-    # u'Hominidae', u'Homininae', u'Homo', u'Homo sapiens']
+  # ['root', 'cellular organisms', 'Eukaryota', 'Opisthokonta', 'Metazoa',
+  # 'Eumetazoa', 'Bilateria', 'Deuterostomia', 'Chordata', 'Craniata',
+  # 'Vertebrata', 'Gnathostomata', 'Teleostomi', 'Euteleostomi',
+  # 'Sarcopterygii', 'Dipnotetrapodomorpha', 'Tetrapoda', 'Amniota',
+  # 'Mammalia', 'Theria', 'Eutheria', 'Boreoeutheria', 'Euarchontoglires',
+  # 'Primates', 'Haplorrhini', 'Simiiformes', 'Catarrhini', 'Hominoidea',
+  # 'Hominidae', 'Homininae', 'Homo', 'Homo sapiens']
 
 
 GTDB taxonomy
 ~~~~~~~~~~~~~
-In the NCBI taxonomy database, each species is assigned a unique numeric taxid. 
-For example, the taxid 9606 refers to Homo sapiens. These taxids serve as 
+
+In the NCBI taxonomy database, each species is assigned a unique numeric taxid.
+For example, the taxid 9606 refers to Homo sapiens. These taxids serve as
 essential keys for tracking lineages within the database.
 
-However, the GTDB database doesn't originally offer numeric taxids like NCBI 
-does. In the GTDBTaxa module, we've introduced taxids for each species to 
-facilitate lineage tracking. These taxids, while not officially recognized in 
-the GTDB database, serve as convenient keys. They help in connecting the lineage 
-and taxonomic ranks within the local database, making it easier for users to 
+However, the GTDB database doesn't originally offer numeric taxids like NCBI
+does. In the GTDBTaxa module, we've introduced taxids for each species to
+facilitate lineage tracking. These taxids, while not officially recognized in
+the GTDB database, serve as convenient keys. They help in connecting the lineage
+and taxonomic ranks within the local database, making it easier for users to
 fetch and relate taxonomic information.
 
 Like NCBITaxa, GTDBTaxa contains similar methods:
 
-- GTDBTaxa.get_rank()
-- GTDBTaxa.get_lineage()
-- GTDBTaxa.get_taxid_translator()
-- GTDBTaxa.get_name_translator()
-- GTDBTaxa.translate_to_names()
-- GTDBTaxa.get_name_lineage()
+.. autosummary::
+
+   GTDBTaxa.get_rank
+   GTDBTaxa.get_lineage
+   GTDBTaxa.get_taxid_translator
+   GTDBTaxa.get_name_translator
+   GTDBTaxa.translate_to_names
+   GTDBTaxa.get_name_lineage
+
 
 Getting descendant taxa
 -----------------------
-Given a taxid or a taxa name from an internal node in the NCBI/GTDB taxonomy tree, 
+
+Given a taxid or a taxa name from an internal node in the NCBI/GTDB taxonomy tree,
 their descendants can be retrieved as follows:
 
-NCBI taxonomy
-Example::
-    # example in NCBI taxonomy
-    from ete4 import NCBITaxa
-    ncbi = NCBITaxa()
+NCBI taxonomy example::
 
-    descendants = ncbi.get_descendant_taxa('Homo')
-    print(ncbi.translate_to_names(descendants))
+  from ete4 import NCBITaxa
+  ncbi = NCBITaxa()
 
-    # [u'Homo heidelbergensis', u'Homo sapiens ssp. Denisova', 
-    # u'Homo sapiens neanderthalensis']
+  descendants = ncbi.get_descendant_taxa('Homo')
+  print(ncbi.translate_to_names(descendants))
 
-    # you can easily ignore subspecies, so only taxa labeled as "species" will be reported:
-    descendants = ncbi.get_descendant_taxa('Homo', collapse_subspecies=True)
-    print(ncbi.translate_to_names(descendants))
+  # ['Homo heidelbergensis', 'Homo sapiens ssp. Denisova',
+  # 'Homo sapiens neanderthalensis']
 
-    # [u'Homo sapiens', u'Homo heidelbergensis']
+  # You can easily ignore subspecies, so only taxa labeled as "species" will be reported:
+  descendants = ncbi.get_descendant_taxa('Homo', collapse_subspecies=True)
+  print(ncbi.translate_to_names(descendants))
 
-    # or even returned as an annotated tree
-    tree = ncbi.get_descendant_taxa('Homo', collapse_subspecies=True, return_tree=True)
+  # ['Homo sapiens', 'Homo heidelbergensis']
 
-    print(tree.to_str(props=['sci_name','taxid']))
+  # or even returned as an annotated tree
+  tree = ncbi.get_descendant_taxa('Homo', collapse_subspecies=True, return_tree=True)
+
+  print(tree.to_str(props=['sci_name','taxid']))
+  #            ╭╴environmental samples,2665952╶╌╴Homo sapiens environmental sample,2665953
+  #            │
+  #            ├╴Homo sapiens,9606
+  # ╴Homo,9605╶┤
+  #            ├╴Homo heidelbergensis,1425170
+  #            │
+  #            ╰╴unclassified Homo,2813598╶╌╴Homo sp.,2813599
+
+GTDB taxonomy example::
+
+  from ete4 import GTDBTaxa
+  gtdb = GTDBTaxa()
+  descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae')
+  print(descendants)
+  # ['GB_GCA_003662765.1', 'GB_GCA_003662805.1', ..., 'GB_GCA_013138615.1']
+
+  # Ignore subspecies, so only taxa labeled as "species" will be reported.
+  descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae', collapse_subspecies=True)
+  print(descendants)
+  # ['s__MP8T-1 sp002825535', 's__MP8T-1 sp003345545', ..., 's__TEKIR-12S sp004524435']
+
+  # Returned as an annotated tree.
+  descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae', collapse_subspecies=True, return_tree=True)
+  print(descendants.to_str(props=['sci_name','rank']))
+  #                                ╭╴s__MP8T-1 sp002825535,species
+  #                                │
+  #                                ├╴s__MP8T-1 sp003345545,species
+  #                                │
+  #              ╭╴g__MP8T-1,genus╶┼╴s__MP8T-1 sp002825465,species
+  #              │                 │
+  #              │                 ├╴s__MP8T-1 sp004524565,species
+  #              │                 │
+  #              │                 ╰╴s__MP8T-1 sp004524595,species
+  #              │
+  #              │                   ╭╴s__SMTZ1-83 sp011364985,species
+  #              │                   │
+  #              ├╴g__SMTZ1-83,genus╶┼╴s__SMTZ1-83 sp011365025,species
+  #              │                   │
+  #              │                   ╰╴s__SMTZ1-83 sp001563325,species
+  #              │
+  #              ├╴g__TEKIR-14,genus╶╌╴s__TEKIR-14 sp004524445,species
+  #              │
+  #              ├╴g__SHMX01,genus╶╌╴s__SHMX01 sp008080745,species
+  #              │
+  #              │               ╭╴s__OWC5 sp003345595,species
+  #              ├╴g__OWC5,genus╶┤
+  # ╴f__Tho[...]╶┤               ╰╴s__OWC5 sp003345555,species
+  #              │
+  #              ├╴g__JACAEL01,genus╶╌╴s__JACAEL01 sp013388835,species
+  #              │
+  #              ├╴g__B65-G9,genus╶╌╴s__B65-G9 sp003662765,species
+  #              │
+  #              │                   ╭╴s__SMTZ1-45 sp001563335,species
+  #              │                   │
+  #              │                   ├╴s__SMTZ1-45 sp011364905,species
+  #              │                   │
+  #              ├╴g__SMTZ1-45,genus╶┼╴s__SMTZ1-45 sp001940705,species
+  #              │                   │
+  #              │                   ├╴s__SMTZ1-45 sp004376265,species
+  #              │                   │
+  #              │                   ╰╴s__SMTZ1-45 sp002825515,species
+  #              │
+  #              ├╴g__WTCK01,genus╶╌╴s__WTCK01 sp013138615,species
+  #              │
+  #              ╰╴g__TEKIR-12S,genus╶╌╴s__TEKIR-12S sp004524435,species
 
-    """
-               ╭╴environmental samples,2665952╶╌╴Homo sapiens environmental sample,2665953
-               │
-               ├╴Homo sapiens,9606
-    ╴Homo,9605╶┤
-               ├╴Homo heidelbergensis,1425170
-               │
-               ╰╴unclassified Homo,2813598╶╌╴Homo sp.,2813599
-    """
-    
-GTDB taxonomy
-Example::
-    from ete4 import GTDBTaxa
-    gtdb = GTDBTaxa()
-    descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae')
-    print(descendants)
-    # ['GB_GCA_003662765.1', 'GB_GCA_003662805.1', 'GB_GCA_003345555.1', 'GB_GCA_003345595.1', 'GB_GCA_001940705.1', 'GB_GCA_001563335.1', 'GB_GCA_011364905.1', 'GB_GCA_004376265.1', 'GB_GCA_002825515.1', 'GB_GCA_001563325.1', 'GB_GCA_011364985.1', 'GB_GCA_011365025.1', 'GB_GCA_004524565.1', 'GB_GCA_004524595.1', 'GB_GCA_002825465.1', 'GB_GCA_002825535.1', 'GB_GCA_003345545.1', 'GB_GCA_004524445.1', 'GB_GCA_013388835.1', 'GB_GCA_008080745.1', 'GB_GCA_004524435.1', 'GB_GCA_013138615.1']
-
-    #ignore subspecies, so only taxa labeled as "species" will be reported
-    descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae', collapse_subspecies=True)
-    
-    print(descendants)
-    
-    #['s__MP8T-1 sp002825535', 's__MP8T-1 sp003345545', 's__MP8T-1 sp002825465', 's__MP8T-1 sp004524565', 's__MP8T-1 sp004524595', 's__SMTZ1-83 sp011364985', 's__SMTZ1-83 sp011365025', 's__SMTZ1-83 sp001563325', 's__TEKIR-14 sp004524445', 's__SHMX01 sp008080745', 's__OWC5 sp003345595', 's__OWC5 sp003345555', 's__JACAEL01 sp013388835', 's__B65-G9 sp003662765', 's__SMTZ1-45 sp001563335', 's__SMTZ1-45 sp011364905', 's__SMTZ1-45 sp001940705', 's__SMTZ1-45 sp004376265', 's__SMTZ1-45 sp002825515', 's__WTCK01 sp013138615', 's__TEKIR-12S sp004524435']
-
-    
-    #returned as an annotated tree
-    descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae', collapse_subspecies=True, return_tree=True)
-    print(descendants.to_str(props=['sci_name','rank']))
-    """
-                                                ╭╴s__MP8T-1 sp002825535,species
-                                                │
-                                                ├╴s__MP8T-1 sp003345545,species
-                                                │
-                            ╭╴g__MP8T-1,genus╶┼╴s__MP8T-1 sp002825465,species
-                            │                 │
-                            │                 ├╴s__MP8T-1 sp004524565,species
-                            │                 │
-                            │                 ╰╴s__MP8T-1 sp004524595,species
-                            │
-                            │                   ╭╴s__SMTZ1-83 sp011364985,species
-                            │                   │
-                            ├╴g__SMTZ1-83,genus╶┼╴s__SMTZ1-83 sp011365025,species
-                            │                   │
-                            │                   ╰╴s__SMTZ1-83 sp001563325,species
-                            │
-                            ├╴g__TEKIR-14,genus╶╌╴s__TEKIR-14 sp004524445,species
-                            │
-                            ├╴g__SHMX01,genus╶╌╴s__SHMX01 sp008080745,species
-                            │
-                            │               ╭╴s__OWC5 sp003345595,species
-                            ├╴g__OWC5,genus╶┤
-    ╴f__Thorarchaeaceae,family╶┤               ╰╴s__OWC5 sp003345555,species
-                            │
-                            ├╴g__JACAEL01,genus╶╌╴s__JACAEL01 sp013388835,species
-                            │
-                            ├╴g__B65-G9,genus╶╌╴s__B65-G9 sp003662765,species
-                            │
-                            │                   ╭╴s__SMTZ1-45 sp001563335,species
-                            │                   │
-                            │                   ├╴s__SMTZ1-45 sp011364905,species
-                            │                   │
-                            ├╴g__SMTZ1-45,genus╶┼╴s__SMTZ1-45 sp001940705,species
-                            │                   │
-                            │                   ├╴s__SMTZ1-45 sp004376265,species
-                            │                   │
-                            │                   ╰╴s__SMTZ1-45 sp002825515,species
-                            │
-                            ├╴g__WTCK01,genus╶╌╴s__WTCK01 sp013138615,species
-                            │
-                            ╰╴g__TEKIR-12S,genus╶╌╴s__TEKIR-12S sp004524435,species
-    """
 
 Getting species tree topology
-----------------------------------
-Getting the taxonomy tree for a given set of species is one of the most useful ways 
-to get all information at once. The method NCBITaxa.get_topology() or GTDBTaxa.get_topology() allows to query your 
-local NCBI/GTDB database and extract the smallest tree that connects all your query taxids. 
-It returns a normal ETE tree in which all nodes, internal or leaves, are annotated for 
-lineage, scientific names, ranks, and so on.
+-----------------------------
 
-NCBI taxonomy
-Example::
-    from ete4 import NCBITaxa
-    ncbi = NCBITaxa()
-
-    tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
-
-    print(tree.to_str(props=["sci_name", "rank"]))
-    """
-                        ╭╴Dendrochirotida,order
-                        │
-                        │                                                                   ╭╴Homo sapiens,species
-    ╴Deuterostomia,clade╶┤                                             ╭╴Homininae,subfamily╶┤
-                        │               ╭╴Euarchontoglires,superorder╶┤                     ╰╴Pan troglodytes,species
-                        │               │                             │
-                        ╰╴Amniota,clade╶┤                             ╰╴Mus musculus,species
-                                        │
-                                        ╰╴Aves,class
-    """
-
-    # all intermediate nodes connecting the species can also be kept in the tree
-    tree = ncbi.get_topology([2, 33208], intermediate_nodes=True)
-    print(tree.to_str(props=["sci_name"]))
-    """
-                        ╭╴Eukaryota╶╌╴Opisthokonta╶╌╴Metazoa
-    ╴cellular organisms╶┤
-                        ╰╴Bacteria
-    """
+Getting the taxonomy tree for a given set of species is one of the
+most useful ways to get all information at once. The methods
+:func:`NCBITaxa.get_topology` or :func:`GTDBTaxa.get_topology` allow
+to query your local NCBI/GTDB database and extract the smallest tree
+that connects all your query taxids. It returns a normal ETE tree in
+which all nodes, internal or leaves, are annotated for lineage,
+scientific names, ranks, and so on.
+
+NCBI taxonomy example::
+
+  from ete4 import NCBITaxa
+  ncbi = NCBITaxa()
+
+  tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
+
+  print(tree.to_str(props=["sci_name", "rank"]))
+  #                      ╭╴Dendrochirotida,order
+  #                      │
+  #                      │                                                                   ╭╴Homo sapiens,species
+  # ╴Deuterostomia,clade╶┤                                             ╭╴Homininae,subfamily╶┤
+  #                      │               ╭╴Euarchontoglires,superorder╶┤                     ╰╴Pan troglodytes,species
+  #                      │               │                             │
+  #                      ╰╴Amniota,clade╶┤                             ╰╴Mus musculus,species
+  #                                      │
+  #                                      ╰╴Aves,class
+
+  # All intermediate nodes connecting the species can also be kept in the tree.
+  tree = ncbi.get_topology([2, 33208], intermediate_nodes=True)
+  print(tree.to_str(props=["sci_name"]))
+  #                     ╭╴Eukaryota╶╌╴Opisthokonta╶╌╴Metazoa
+  # ╴cellular organisms╶┤
+  #                     ╰╴Bacteria
+
+GTDB taxonomy example::
+
+  from ete4 import GTDBTaxa
+  gtdb = GTDBTaxa()
+
+  tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae"])
+  print(tree.to_str(props=['sci_name', 'rank']))
+  #                                         ╭╴p__Huberarchaeota,phylum
+  #               ╭╴d__Archaea,superkingdom╶┤
+  # ╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
+  #               │
+  #               ╰╴o__Peptococcales,order
+
+  # All intermediate nodes connecting the species can also be kept in the tree.
+  tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae"], intermediate_nodes=True, collapse_subspecies=True, annotate=True)
+  print(tree.to_str(props=['sci_name', 'rank']))
+  #                                         ╭╴p__Huberarchaeota,phylum
+  #               ╭╴d__Archaea,superkingdom╶┤
+  # ╴root,no rank╶┤                         ╰╴p__Thermoproteota,phylum╶╌╴c__Korarchaeia,class╶╌╴o__Korarchaeales,order╶╌╴f__Korarchaeaceae,family
+  #               │
+  #               ╰╴d__Bacteria,superkingdom╶╌╴p__Firmicutes_B,phylum╶╌╴c__Peptococcia,class╶╌╴o__Peptococcales,order
 
-GTDB taxonomy
-Example::
-    from ete4 import GTDBTaxa
-    gtdb = GTDBTaxa()
-
-    tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae"])
-    print(tree.to_str(props=['sci_name', 'rank']))
-
-    """
-                                            ╭╴p__Huberarchaeota,phylum
-                ╭╴d__Archaea,superkingdom╶┤
-    ╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
-                │
-                ╰╴o__Peptococcales,order
-
-    """
-
-    # all intermediate nodes connecting the species can also be kept in the tree
-    tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae"], intermediate_nodes=True, collapse_subspecies=True, annotate=True)
-    print(tree.to_str(props=['sci_name', 'rank']))
-    """
-                                            ╭╴p__Huberarchaeota,phylum
-                ╭╴d__Archaea,superkingdom╶┤
-    ╴root,no rank╶┤                         ╰╴p__Thermoproteota,phylum╶╌╴c__Korarchaeia,class╶╌╴o__Korarchaeales,order╶╌╴f__Korarchaeaceae,family
-                │
-                ╰╴d__Bacteria,superkingdom╶╌╴p__Firmicutes_B,phylum╶╌╴c__Peptococcia,class╶╌╴o__Peptococcales,order
-    """
 
 Automatic tree annotation using NCBI/GTDB taxonomy
----------------------------------------------
-NCBI/GTDB taxonomy annotation consists of adding additional information to any internal a leaf node 
-in a give user tree. Only an property containing the taxid associated to each node 
-is required for the nodes in the query tree. The annotation process will add the 
-following features to the nodes:
+--------------------------------------------------
+
+NCBI/GTDB taxonomy annotation consists of adding additional
+information to any internal or leaf node in a tree. Only a property
+containing the taxid associated to each node is required for the nodes
+in the query tree. The annotation process will add the following
+features to the nodes:
 
 - sci_name
 - taxid
@@ -346,53 +361,50 @@ following features to the nodes:
 - lineage
 - rank
 
-Note that, for internal nodes, taxid can be automatically inferred based on their sibling 
-nodes. The easiest way to annotate a tree is to use a PhyloTree instance where the species 
-name attribute is transparently used as the taxid attribute. Note that 
-the :PhyloNode:`annotate_ncbi_taxa`: or :PhyloNode:`annotate_gtdb_taxa`: function will also return the used name, lineage and 
-rank translators.
+Note that, for internal nodes, taxid can be automatically inferred
+based on their sibling nodes. The easiest way to annotate a tree is to
+use a PhyloTree instance where the species name attribute is
+transparently used as the taxid attribute. Note that the
+:func:`~PhyloTree.annotate_ncbi_taxa` or
+:func:`~PhyloTree.annotate_gtdb_taxa` function will also return the
+used name, lineage and rank translators.
 
-Remember that species names in PhyloTree instances are automatically extracted from leaf names. The parsing method can be easily adapted to any formatting:
+Remember that species names in PhyloTree instances are automatically
+extracted from leaf names. The parsing method can be easily adapted to
+any formatting:
 
-NCBI taxonomy
-Example::
-    from ete4 import PhyloTree
+NCBI taxonomy example::
 
-    # load the whole leaf name as species taxid
-    tree = PhyloTree('((9606, 9598), 10090);', sp_naming_function=lambda name: name)
-    tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
+  from ete4 import PhyloTree
 
+  # Load the whole leaf name as species taxid.
+  tree = PhyloTree('((9606, 9598), 10090);', sp_naming_function=lambda name: name)
+  tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
 
-    # split names by '|' and return the first part as the species taxid
-    tree = PhyloTree('((9606|protA, 9598|protA), 10090|protB);', sp_naming_function=lambda name: name.split('|')[0])
-    tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
+  # Split names by '|' and return the first part as the species taxid.
+  tree = PhyloTree('((9606|protA, 9598|protA), 10090|protB);', sp_naming_function=lambda name: name.split('|')[0])
+  tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
 
-    print(tree.to_str(props=["name", "sci_name", "taxid"]))
+  print(tree.to_str(props=["name", "sci_name", "taxid"]))
+  #                                                             ╭╴9606|protA,Homo sapiens,9606
+  #                                  ╭╴(empty),Homininae,207598╶┤
+  # ╴(empty),Euarchontoglires,314146╶┤                          ╰╴9598|protA,Pan troglodytes,9598
+  #                                  │
+  #                                  ╰╴10090|protB,Mus musculus,10090
 
-    """
-                                                                ╭╴9606|protA,Homo sapiens,9606
-                                     ╭╴(empty),Homininae,207598╶┤
-    ╴(empty),Euarchontoglires,314146╶┤                          ╰╴9598|protA,Pan troglodytes,9598
-                                     │
-                                     ╰╴10090|protB,Mus musculus,10090
-    """
-
-GTDB taxonomy
-Example::
-    from ete4 import PhyloTree
+GTDB taxonomy example::
 
-    # load the whole leaf name as species taxid
-    newick = '((p__Huberarchaeota,f__Korarchaeaceae)d__Archaea,o__Peptococcales);'
+  from ete4 import PhyloTree
 
-    tree= PhyloTree(newick)
-    tax2name, tax2track, tax2rank = gtdb.annotate_tree(tree, taxid_attr="name")
+  # Load the whole leaf name as species taxid.
+  newick = '((p__Huberarchaeota,f__Korarchaeaceae)d__Archaea,o__Peptococcales);'
 
-    print(tree.to_str(props=['sci_name', 'rank']))
+  tree = PhyloTree(newick)
+  tax2name, tax2track, tax2rank = gtdb.annotate_tree(tree, taxid_attr="name")
 
-    """
-                                            ╭╴p__Huberarchaeota,phylum
-                  ╭╴d__Archaea,superkingdom╶┤
-    ╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
-                  │
-                  ╰╴o__Peptococcales,order
-    """
\ No newline at end of file
+  print(tree.to_str(props=['sci_name', 'rank']))
+  #                                         ╭╴p__Huberarchaeota,phylum
+  #               ╭╴d__Archaea,superkingdom╶┤
+  # ╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
+  #               │
+  #               ╰╴o__Peptococcales,order
diff --git a/genindex.html b/genindex.html
index 45b5d0d26..bb1482316 100644
--- a/genindex.html
+++ b/genindex.html
@@ -85,6 +85,8 @@ 
    _
    
         
  • (DrawerCirc method)
 
    • 
         
  • (Face method)
+
    • 
+        
  • (GTDBTaxa method)
 
    • 
         
  • (HTMLFace method)
 
    • 
@@ -158,7 +160,7 @@ 
    _
    
 
         
  • (LegendFace method)
 
    • 
-        
  • (NCBITaxa method)
+        
  • (NCBITaxa method)
 
    • 
         
  • (NodeStyle method)
 
    • 
@@ -237,10 +239,10 @@ 
    A
    
 
       
  • add_prop() (Tree method)
 
    • 
-  
-  
+  
-      
  • get_broken_branches() (NCBITaxa method)
+      
  • get_broken_branches() (GTDBTaxa method)
+
+      
    • 
       
  • get_cached_content() (Tree method)
 
    • 
       
  • get_children() (Tree method)
@@ -839,8 +842,12 @@ 
    G
    
 
    • 
       
  • get_commands() (in module ete4.parser.nexus)
 
    • 
-      
  • get_common_names() (NCBITaxa method)
+      
  • get_common_names() (GTDBTaxa method)
+
+      
    • 
       
  • get_content() (AttrFace method)
 
       
-  
+  
 
@@ -1071,8 +1110,6 @@ 
    I
    
         
  • (DrawerRect method)
 
    • 
       
-      
  • is_taxadb_up_to_date() (in module ete4.ncbi_taxonomy.ncbiquery)
-
    • 
       
  • iter_entries() (SeqGroup method)
 
    • 
       
  • iter_prepostorder() (Tree method)
@@ -1252,8 +1289,6 @@ 
    M
    
         
  • ete4.core.operations
 
    • 
         
  • ete4.core.seqgroup
-
    • 
-        
  • ete4.ncbi_taxonomy.ncbiquery
 
    • 
         
  • ete4.parser.newick
 
    • 
@@ -1320,7 +1355,7 @@ 
    N
    
       
       
  • ncbi_compare() (PhyloTree method)
 
    • 
-      
  • NCBITaxa (class in ete4.ncbi_taxonomy.ncbiquery)
+      
  • NCBITaxa (class in ete4)
 
    • 
       
  • NewickError
 
    • 
@@ -1652,14 +1687,18 @@ 
    T
    
       
       
  • touch_and_get() (in module ete4.smartview.gui.server)
 
    • 
-      
  • translate_to_names() (NCBITaxa method)
+      
  • translate_to_names() (GTDBTaxa method)
+
+      
    • 
       
  • traverse() (Tree method)
-
    • 
-      
  • tree (AppTree attribute)
 
    • 
   
   
-  
+  
 
 
diff --git a/index.html b/index.html
index 994c4447e..dd4474d20 100644
--- a/index.html
+++ b/index.html
@@ -53,6 +53,7 @@ 
    Welcome to ETE’s documentation!Working with the Tree structure
 
  • Phylogenetic trees
    • 
 
  • Programmable tree drawing
    • 
+
  • Taxonomy databases
    • 
 
 
 
  • Reference Guide
diff --git a/objects.inv b/objects.inv
index 2af9d160f..b63808f0d 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/py-modindex.html b/py-modindex.html
index 636cf500f..b45468efd 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -66,11 +66,6 @@ 
    Python Module Index
    
           
        ete4.core.seqgroup
        
-     
-       
-          
-       ete4.ncbi_taxonomy.ncbiquery
-       
      
        
           
diff --git a/reference/index.html b/reference/index.html
index da4e002a6..02bcdff04 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -16,7 +16,7 @@
     
     
     
-    
+    
    
   
   
@@ -69,8 +69,8 @@ 
    Reference GuidePhylogenetic trees
 
    • 
 
  • Clustering
      
@@ -81,9 +81,9 @@ 
      Reference GuideSeqGroup
 
    
 
    • 
-
  • NCBITaxa
diff --git a/reference/reference_operations.html b/reference/reference_operations.html
index 0611491ce..98d04d838 100644
--- a/reference/reference_operations.html
+++ b/reference/reference_operations.html
@@ -274,7 +274,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
diff --git a/reference/reference_parsers.html b/reference/reference_parsers.html
index 1194a8f02..4ebb3b80c 100644
--- a/reference/reference_parsers.html
+++ b/reference/reference_parsers.html
@@ -228,7 +228,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
diff --git a/reference/reference_phylo.html b/reference/reference_phylo.html
index 0160b42f5..919fee9b7 100644
--- a/reference/reference_phylo.html
+++ b/reference/reference_phylo.html
@@ -35,6 +35,8 @@
             
   
    
 
    Phylogenetic trees
    
+
    
+
    PhyloTree
    
 
    
 
    
 class PhyloTree(newick=None, children=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species>, parser=None)[source]
    
@@ -329,6 +331,9 @@ 
    Phylogenetic trees
+
    EvolEvent
    
 
    
 
    
 class EvolEvent[source]
    
@@ -340,6 +345,7 @@ 
    Phylogenetic treesnode : link to the event node in the tree
    
 
    
 
+
    
 
    
 
 
@@ -371,7 +377,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
diff --git a/reference/reference_seqgroup.html b/reference/reference_seqgroup.html
index af24fa11a..d1f2087b7 100644
--- a/reference/reference_seqgroup.html
+++ b/reference/reference_seqgroup.html
@@ -15,7 +15,7 @@
     
     
     
-    
+    
     
    
   
@@ -144,7 +144,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
@@ -157,7 +157,7 @@ 
    Related Topics
    
   
  • Documentation overview
    • 
 
diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html
index 3109e0a7d..0e4172006 100644
--- a/reference/reference_smartview.html
+++ b/reference/reference_smartview.html
@@ -16,7 +16,7 @@
     
     
     
-    
+    
    
   
   
@@ -86,7 +86,7 @@ 
    Smartview (web graphi
 
 
    
 
    
-class AppTree(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f005af47e20> = None, searches: dict = None)[source]
    
+class AppTree(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f81c0547e20> = None, searches: dict = None)[source]
 
    
 
    
 __init__(tree: Tree = None, name: str = None, style: TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, initialized: bool = False, selected: dict = None, active: namedtuple = None, searches: dict = None) → None
    
@@ -2380,7 +2380,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
@@ -2392,7 +2392,7 @@ 
    Related Topics
    
 
      
   
    • Documentation overview
      • 
diff --git a/reference/reference_ncbi.html b/reference/reference_taxonomy.html
similarity index 50%
rename from reference/reference_ncbi.html
rename to reference/reference_taxonomy.html
index 7b3d98439..e8e2fc742 100644
--- a/reference/reference_ncbi.html
+++ b/reference/reference_taxonomy.html
@@ -5,7 +5,7 @@
     
     
 
-    NCBITaxa — ETE Toolkit 4.0.0-beta documentation
+    Taxonomy databases — ETE Toolkit 4.0.0-beta documentation
     
     
     
@@ -33,15 +33,17 @@
 
           
      
             
-  
      
-
      NCBITaxa
      
+  
      
+
      Taxonomy databases
      
+
      
+
      NCBITaxa
      
 
      
-
      
-class NCBITaxa(dbfile=None, taxdump_file=None, memory=False, update=True)[source]
      
+
      
+class NCBITaxa(dbfile=None, taxdump_file=None, memory=False, update=True)[source]
      
 
      A local transparent connector to the NCBI taxonomy database.
      
 
      
-
      
-__init__(dbfile=None, taxdump_file=None, memory=False, update=True)[source]
      
+
      
+__init__(dbfile=None, taxdump_file=None, memory=False, update=True)[source]
      
 
      Open and keep a connection to the NCBI taxonomy database.
      
 
      If it is not present in the system, it will download the
 database from the NCBI site first, and convert it to ete’s
@@ -49,8 +51,8 @@
 
      
 
 
      
-
      
-annotate_tree(t, taxid_attr='name', tax2name=None, tax2track=None, tax2rank=None)[source]
      
+
      
+annotate_tree(t, taxid_attr='name', tax2name=None, tax2track=None, tax2rank=None)[source]
      
 
      Annotate a tree containing taxids as leaf names.
      
 
      The annotation adds the properties: ‘taxid’, ‘sci_name’,
 ‘lineage’, ‘named_lineage’ and ‘rank’.
      
@@ -70,29 +72,29 @@
 
      
 
 
      
-
      
-get_broken_branches(t, taxa_lineages, n2content=None)[source]
      
+
      
+get_broken_branches(t, taxa_lineages, n2content=None)[source]
      
 
      Returns a list of NCBI lineage names that are not monophyletic in the
 provided tree, as well as the list of affected branches and their size.
      
 
      CURRENTLY EXPERIMENTAL
      
 
      
 
 
      
-
      
-get_common_names(taxids)[source]
      
+
      
+get_common_names(taxids)[source]
      
 
      
 
 
      
-
      
-get_descendant_taxa(parent, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, return_tree=False)[source]
      
+
      
+get_descendant_taxa(parent, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, return_tree=False)[source]
      
 
      Return list of descendant taxids of the given parent.
      
 
      Parent can be given as taxid or scientific species name.
      
 
      If intermediate_nodes=True, the list will also have the internal nodes.
      
 
      
 
 
      
-
      
-get_fuzzy_name_translation(name, sim=0.9)[source]
      
+
      
+get_fuzzy_name_translation(name, sim=0.9)[source]
      
 
      Return taxid, species name and match score from the NCBI database.
      
 
      The results are for the best match for name in the NCBI
 database of taxa names, with a word similarity >= sim.
      
@@ -107,41 +109,41 @@
 
      
 
 
      
-
      
-get_lineage(taxid)[source]
      
+
      
+get_lineage(taxid)[source]
      
 
      Return lineage track corresponding to the given taxid.
      
 
      The lineage track is a hierarchically sorted list of parent taxids.
      
 
      
 
 
      
-
      
-get_lineage_translator(taxids)[source]
      
+
      
+get_lineage_translator(taxids)[source]
      
 
      Return dict with lineage tracks corresponding to the given taxids.
      
 
      The lineage tracks are a hierarchically sorted list of parent taxids.
      
 
      
 
 
      
-
      
-get_name_translator(names)[source]
      
+
      
+get_name_translator(names)[source]
      
 
      Return dict with taxids corresponding to the given scientific names.
      
 
      Exact name match is required for translation.
      
 
      
 
 
      
-
      
-get_rank(taxids)[source]
      
+
      
+get_rank(taxids)[source]
      
 
      Return dict with NCBI taxonomy ranks for each list of taxids.
      
 
      
 
 
      
-
      
-get_taxid_translator(taxids, try_synonyms=True)[source]
      
+
      
+get_taxid_translator(taxids, try_synonyms=True)[source]
      
 
      Return dict with the scientific names corresponding to the taxids.
      
 
      
 
 
      
-
      
-get_topology(taxids, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, annotate=True)[source]
      
+
      
+get_topology(taxids, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, annotate=True)[source]
      
 
      Return the minimal pruned NCBI taxonomy tree containing taxids.
      
 
      
 
      Parameters:
      
@@ -163,14 +165,14 @@
 
      
 
 
      
-
      
-translate_to_names(taxids)[source]
      
+
      
+translate_to_names(taxids)[source]
      
 
      Return list of scientific names corresponding to taxids.
      
 
      
 
 
      
-
      
-update_taxonomy_database(taxdump_file=None)[source]
      
+
      
+update_taxonomy_database(taxdump_file=None)[source]
      
 
      Update the ncbi taxonomy database.
      
 
      It does it by downloading and parsing the latest
 taxdump.tar.gz file from the NCBI site.
      
@@ -184,13 +186,145 @@
 
 
      
 
-
      
-
      
-is_taxadb_up_to_date(dbfile='/home/runner/.local/share/ete/taxa.sqlite')[source]
      
-
      Return True if a valid and up-to-date taxa.sqlite database exists.
      
-
      If dbfile is not specified, DEFAULT_TAXADB is assumed.
      
+
      
+
      
+
      GTDBTaxa
      
+
      
+
      
+class GTDBTaxa(dbfile=None, taxdump_file=None, memory=False)[source]
      
+
      Local transparent connector to the GTDB taxonomy database.
      
+
      
+
      
+__init__(dbfile=None, taxdump_file=None, memory=False)[source]
      
+
      
+
+
      
+
      
+annotate_tree(t, taxid_attr='name', tax2name=None, tax2track=None, tax2rank=None)[source]
      
+
      Annotate a tree containing taxids as leaf names.
      
+
      It annotates by adding the properties ‘taxid’, ‘sci_name’,
+‘lineage’, ‘named_lineage’ and ‘rank’.
      
+
      
+
      Parameters:
      
+
        
+
      • t – Tree to annotate.
        • 
+
      • taxid_attr – Node attribute (property) containing the
+taxid number associated to each node (i.e. species in
+PhyloTree instances).
        • 
+
      • tax2rank (tax2name, tax2track,) – Pre-calculated
+dictionaries with translations from taxid number to names,
+track lineages and ranks.
        • 
+
      
+
      
+
      
+
      
+
+
      
+
      
+get_broken_branches(t, taxa_lineages, n2content=None)[source]
      
+
      Returns a list of GTDB lineage names that are not monophyletic in the
+provided tree, as well as the list of affected branches and their size.
+CURRENTLY EXPERIMENTAL
      
+
      
+
+
      
+
      
+get_common_names(taxids)[source]
      
+
      
+
+
      
+
      
+get_descendant_taxa(parent, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, return_tree=False)[source]
      
+
      given a parent taxid or scientific species name, returns a list of all its descendants taxids.
+If intermediate_nodes is set to True, internal nodes will also be dumped.
      
+
      
+
+
      
+
      
+get_lineage(taxid)[source]
      
+
      Given a valid taxid number, return its corresponding lineage track as a
+hierarchically sorted list of parent taxids.
      
+
      
+
+
      
+
      
+get_lineage_translator(taxids)[source]
      
+
      Given a valid taxid number, return its corresponding lineage track as a
+hierarchically sorted list of parent taxids.
      
+
      
+
+
      
+
      
+get_name_lineage(taxnames)[source]
      
+
      Given a valid taxname, return its corresponding lineage track as a
+hierarchically sorted list of parent taxnames.
      
+
      
+
+
      
+
      
+get_name_translator(names)[source]
      
+
      Given a list of taxid scientific names, returns a dictionary translating them into their corresponding taxids.
+Exact name match is required for translation.
      
 
      
 
+
      
+
      
+get_rank(taxids)[source]
      
+
      Return dictionary converting taxids to their GTDB taxonomy rank.
      
+
      
+
+
      
+
      
+get_taxid_translator(taxids, try_synonyms=True)[source]
      
+
      Given a list of taxids, returns a dictionary with their corresponding
+scientific names.
      
+
      
+
+
      
+
      
+get_topology(taxnames, intermediate_nodes=False, rank_limit=None, collapse_subspecies=False, annotate=True)[source]
      
+
      Return minimal pruned GTDB taxonomy tree containing all given taxids.
      
+
      
+
      Parameters:
      
+
        
+
      • intermediate_nodes – If True, single child nodes
+representing the complete lineage of leaf nodes are kept.
+Otherwise, the tree is pruned to contain the first common
+ancestor of each group.
        • 
+
      • rank_limit – If valid NCBI rank name is provided, the
+tree is pruned at that given level. For instance, use
+rank=”species” to get rid of sub-species or strain leaf
+nodes.
        • 
+
      • collapse_subspecies – If True, any item under the
+species rank will be collapsed into the species upper
+node.
        • 
+
      
+
      
+
      
+
      
+
+
      
+
      
+translate_to_names(taxids)[source]
      
+
      Given a list of taxid numbers, returns another list with their corresponding scientific names.
      
+
      
+
+
      
+
      
+update_taxonomy_database(taxdump_file=None)[source]
      
+
      Update the GTDB taxonomy database.
      
+
      It updates it by downloading and parsing the latest
+gtdbtaxdump.tar.gz file.
      
+
      
+
      Parameters:
      
+
      taxdump_file – Alternative location of gtdbtaxdump.tar.gz.
      
+
      
+
      
+
      
+
+
      
+
+
      
 
      
 
 
@@ -222,7 +356,7 @@ 
      Navigation
      
 
    • Phylogenetic trees
      • 
 
    • Clustering
      • 
 
    • Multiple Sequence Alignments (SeqGroup)
      • 
-
    • NCBITaxa
      • 
+
    • Taxonomy databases
      • 
 
    • Smartview (web graphics)
      • 
 
    • Treeview (qt graphics)
      • 
 
    
@@ -270,7 +404,7 @@ 
    Quick search
    
       & Alabaster 0.7.13
       
       |
-      Page source
     
    
 
diff --git a/reference/reference_tree.html b/reference/reference_tree.html
index 00dc70c1a..e13356545 100644
--- a/reference/reference_tree.html
+++ b/reference/reference_tree.html
@@ -1129,7 +1129,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
diff --git a/reference/reference_treeview.html b/reference/reference_treeview.html
index 9e4b9d5b0..c4c0268e2 100644
--- a/reference/reference_treeview.html
+++ b/reference/reference_treeview.html
@@ -86,7 +86,7 @@ 
    Navigation
    
 
  • Phylogenetic trees
    • 
 
  • Clustering
    • 
 
  • Multiple Sequence Alignments (SeqGroup)
    • 
-
  • NCBITaxa
    • 
+
  • Taxonomy databases
    • 
 
  • Smartview (web graphics)
    • 
 
  • Treeview (qt graphics)
    • 
 
diff --git a/searchindex.js b/searchindex.js
index 6ff0ee712..cc94ffd91 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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"can-i-control-the-order-in-which-nodes-are-visited"]], "Reading and writing": [[1, "reading-and-writing"]], "How do I load a tree with internal node names or support?": [[1, "how-do-i-load-a-tree-with-internal-node-names-or-support"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "Tree visualization": [[1, "tree-visualization"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "Can the visualization of trees with very unbalanced tree branches be improved?": [[1, "can-the-visualization-of-trees-with-very-unbalanced-tree-branches-be-improved"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Contents:": [[2, null]], "Indices and tables": [[2, "indices-and-tables"]], "Reference Guide": [[3, "reference-guide"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "NCBITaxa": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "Tree operations": [[6, "module-ete4.core.operations"]], "Parsers": [[7, "parsers"]], "Newick": [[7, "module-ete4.parser.newick"]], "Nexus": [[7, "module-ete4.parser.nexus"]], "Phylogenetic trees": [[8, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "Multiple Sequence Alignments (SeqGroup)": [[9, "module-ete4.core.seqgroup"]], "Smartview (web graphics)": [[10, "smartview-web-graphics"]], "Server": [[10, "module-ete4.smartview.gui.server"]], "Renderer": [[10, "renderer"]], "Drawer": [[10, "module-ete4.smartview.renderer.drawer"]], "Draw helpers": [[10, "module-ete4.smartview.renderer.draw_helpers"]], "Faces": [[10, "module-ete4.smartview.renderer.faces"], [12, "faces"]], "Face positions": [[10, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[10, "module-ete4.smartview.renderer.nodestyle"], [12, "nodestyle"]], "TreeLayout": [[10, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[10, "module-ete4.smartview.renderer.treestyle"], [12, "treestyle"]], "Layouts": [[10, "layouts"]], "context": [[10, "module-ete4.smartview.renderer.layouts.context_layouts"]], "default": [[10, "module-ete4.smartview.renderer.layouts.default_layouts"]], "domain": [[10, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "eggnog6": [[10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "etecompare": [[10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "evocell": [[10, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "evol_events": [[10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ncbi_taxonomy": [[10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "phylocloud_egg5": [[10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "seq": [[10, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "spongilla": [[10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "staple": [[10, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "Tree (main class)": [[11, "tree-main-class"]], "Treeview (qt graphics)": [[12, "treeview-qt-graphics"]], "Tutorial": [[13, "tutorial"]], "Programmable tree drawing": [[14, "programmable-tree-drawing"]], "Overview": [[14, "overview"], [15, "overview"], [16, "overview"]], "Interactive visualization of trees": [[14, "interactive-visualization-of-trees"]], "Rendering trees as images": [[14, "rendering-trees-as-images"]], "Customizing the aspect of trees": [[14, "customizing-the-aspect-of-trees"]], "Tree style": [[14, "tree-style"]], "Show leaf node names, branch length and branch support": [[14, "show-leaf-node-names-branch-length-and-branch-support"]], "Change branch length scale (zoom in x)": [[14, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[14, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[14, "rotate-a-tree"]], "Circular tree in 180 degrees": [[14, "circular-tree-in-180-degrees"]], "Add legend and title": [[14, "add-legend-and-title"]], "Node style": [[14, "node-style"]], "Node faces": [[14, "node-faces"]], "Faces position": [[14, "faces-position"]], "Face properties": [[14, "face-properties"]], "Layout functions": [[14, "layout-functions"]], "Combining styles, faces and layouts": [[14, "combining-styles-faces-and-layouts"]], "Fixed node styles": [[14, "fixed-node-styles"]], "Node backgrounds": [[14, "node-backgrounds"]], "Img faces": [[14, "img-faces"]], "Bubble tree maps": [[14, "bubble-tree-maps"]], "Trees within trees": [[14, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[14, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[14, "creating-your-custom-interactive-faces"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[15, "implementation"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Connecting with Taxonomy Databases": [[16, "connecting-with-taxonomy-databases"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[16, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[16, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Getting taxid information": [[16, "getting-taxid-information"]], "NCBI taxonomy": [[16, "ncbi-taxonomy"]], "GTDB taxonomy": [[16, "gtdb-taxonomy"]], "Getting descendant taxa": [[16, "getting-descendant-taxa"]], "Getting species tree topology": [[16, "getting-species-tree-topology"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[16, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "Working with the Tree structure": [[17, "working-with-the-tree-structure"]], "Trees": [[17, "trees"]], "Reading and writing newick trees": [[17, "reading-and-writing-newick-trees"]], "Creating a tree": [[17, "creating-a-tree"]], "Reading newick trees": [[17, "reading-newick-trees"]], "Writing newick trees": [[17, "writing-newick-trees"]], "Understanding ETE trees": [[17, "understanding-ete-trees"]], "Basic tree attributes": [[17, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[17, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[17, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[17, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[17, "traversing-browsing-trees"]], "Advanced traversing": [[17, "advanced-traversing"]], "Collapsing nodes while traversing": [[17, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[17, "iterators-or-lists"]], "Finding nodes by their properties": [[17, "finding-nodes-by-their-properties"]], "Search_all nodes matching a given criteria": [[17, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria (iteration)": [[17, "search-nodes-matching-a-given-criteria-iteration"]], "Find the first common ancestor": [[17, "find-the-first-common-ancestor"]], "Custom searching functions": [[17, "custom-searching-functions"]], "Shortcuts": [[17, "shortcuts"]], "Checking the monophyly of properties within a tree": [[17, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[17, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[17, "node-annotation"]], "Comparing trees": [[17, "comparing-trees"]], "Distances between trees": [[17, "distances-between-trees"]], "Robinson-Foulds distance": [[17, "robinson-foulds-distance"]], "Modifying tree topology": [[17, "modifying-tree-topology"]], "Creating trees from scratch": [[17, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[17, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[17, "pruning-trees"]], "Concatenating trees": [[17, "concatenating-trees"]], "Copying (duplicating) trees": [[17, "copying-duplicating-trees"]], "Solving multifurcations": [[17, "solving-multifurcations"]], "Tree rooting": [[17, "tree-rooting"]], "Working with branch distances": [[17, "working-with-branch-distances"]], "Getting distances between nodes": [[17, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[17, "getting-midpoint-outgroup"]]}, "indexentries": {"clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree"]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__"]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation"]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree"]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn"]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette"]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist"]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist"]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles"]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable"]], "module": [[4, "module-ete4.clustering.clustertree"], [5, "module-ete4.ncbi_taxonomy.ncbiquery"], [6, "module-ete4.core.operations"], [7, "module-ete4.parser.newick"], [7, "module-ete4.parser.nexus"], [9, "module-ete4.core.seqgroup"], [10, "module-ete4.smartview.gui.server"], [10, "module-ete4.smartview.renderer.draw_helpers"], [10, "module-ete4.smartview.renderer.drawer"], [10, "module-ete4.smartview.renderer.face_positions"], [10, "module-ete4.smartview.renderer.faces"], [10, "module-ete4.smartview.renderer.layouts.context_layouts"], [10, "module-ete4.smartview.renderer.layouts.default_layouts"], [10, "module-ete4.smartview.renderer.layouts.domain_layouts"], [10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"], [10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"], [10, "module-ete4.smartview.renderer.layouts.evocell_layouts"], [10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"], [10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"], [10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"], [10, "module-ete4.smartview.renderer.layouts.seq_layouts"], [10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"], [10, "module-ete4.smartview.renderer.layouts.staple_layouts"], [10, "module-ete4.smartview.renderer.nodestyle"], [10, "module-ete4.smartview.renderer.treelayout"], [10, "module-ete4.smartview.renderer.treestyle"], [12, "module-treeview"]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile"]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function"]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette"]], "ncbitaxa (class in ete4.ncbi_taxonomy.ncbiquery)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa"]], "__init__() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.__init__"]], "annotate_tree() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.annotate_tree"]], "ete4.ncbi_taxonomy.ncbiquery": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "get_broken_branches() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_broken_branches"]], "get_common_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_common_names"]], "get_descendant_taxa() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage"]], "get_lineage_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage_translator"]], "get_name_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_name_translator"]], "get_rank() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_rank"]], "get_taxid_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_taxid_translator"]], "get_topology() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_topology"]], "is_taxadb_up_to_date() (in module ete4.ncbi_taxonomy.ncbiquery)": [[5, "ete4.ncbi_taxonomy.ncbiquery.is_taxadb_up_to_date"]], "translate_to_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.update_taxonomy_database"]], "walker (class in ete4.core.operations)": [[6, "ete4.core.operations.Walker"]], "add_next_branch() (walker method)": [[6, "ete4.core.operations.Walker.add_next_branch"]], "assert_root_consistency() (in module ete4.core.operations)": [[6, "ete4.core.operations.assert_root_consistency"]], "common_ancestor() (in module ete4.core.operations)": [[6, "ete4.core.operations.common_ancestor"]], "ete4.core.operations": [[6, "module-ete4.core.operations"]], "first_visit (walker property)": [[6, "ete4.core.operations.Walker.first_visit"]], "go_back() (walker method)": [[6, "ete4.core.operations.Walker.go_back"]], "has_unvisited_branches (walker property)": [[6, "ete4.core.operations.Walker.has_unvisited_branches"]], "insert_intermediate() (in module ete4.core.operations)": [[6, "ete4.core.operations.insert_intermediate"]], "join_branch() (in module ete4.core.operations)": [[6, "ete4.core.operations.join_branch"]], "ladderize() (in module ete4.core.operations)": [[6, "ete4.core.operations.ladderize"]], "maybe_convert_internal_nodes_to_support() (in module ete4.core.operations)": [[6, "ete4.core.operations.maybe_convert_internal_nodes_to_support"]], "move() (in module ete4.core.operations)": [[6, "ete4.core.operations.move"]], "node (walker property)": [[6, "ete4.core.operations.Walker.node"]], "node_id (walker property)": [[6, "ete4.core.operations.Walker.node_id"]], "populate() (in module ete4.core.operations)": [[6, "ete4.core.operations.populate"]], "rehang() (in module ete4.core.operations)": [[6, "ete4.core.operations.rehang"]], "remove() (in module ete4.core.operations)": [[6, "ete4.core.operations.remove"]], "set_outgroup() (in module ete4.core.operations)": [[6, "ete4.core.operations.set_outgroup"]], "sort() (in module ete4.core.operations)": [[6, "ete4.core.operations.sort"]], "swap_props() (in module ete4.core.operations)": [[6, "ete4.core.operations.swap_props"]], "to_ultrametric() (in module ete4.core.operations)": [[6, "ete4.core.operations.to_ultrametric"]], "update_size() (in module ete4.core.operations)": [[6, "ete4.core.operations.update_size"]], "update_sizes_all() (in module ete4.core.operations)": [[6, "ete4.core.operations.update_sizes_all"]], "update_sizes_from() (in module ete4.core.operations)": [[6, "ete4.core.operations.update_sizes_from"]], "walk() (in module ete4.core.operations)": [[6, "ete4.core.operations.walk"]], "newickerror": [[7, "ete4.parser.newick.NewickError"]], "nexuserror": [[7, "ete4.parser.nexus.NexusError"]], "apply_translations() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.apply_translations"]], "content_repr() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.content_repr"]], "dump() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.dump"]], "dumps() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.dumps"]], "error() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.error"]], "ete4.parser.newick": [[7, "module-ete4.parser.newick"]], "ete4.parser.nexus": [[7, "module-ete4.parser.nexus"]], "get_commands() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_commands"]], "get_extended_props() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.get_extended_props"]], "get_props() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.get_props"]], "get_section() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_section"]], "get_sections() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_sections"]], "get_trees() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.get_trees"]], "load() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.load"]], "load() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.load"]], "loads() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.loads"]], "loads() (in module ete4.parser.nexus)": [[7, "ete4.parser.nexus.loads"]], "make_parser() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.make_parser"]], "prop_repr() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.prop_repr"]], "quote() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.quote"]], "read_content() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.read_content"]], "read_nodes() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.read_nodes"]], "repr_short() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.repr_short"]], "skip_quoted_name() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.skip_quoted_name"]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.skip_spaces_and_comments"]], "unquote() (in module ete4.parser.newick)": [[7, "ete4.parser.newick.unquote"]], "evolevent (class in ete4.phylo)": [[8, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[8, "ete4.PhyloTree"]], "__init__() (phylotree method)": [[8, "ete4.PhyloTree.__init__"]], "annotate_gtdb_taxa() (phylotree method)": [[8, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[8, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[8, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[8, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[8, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[8, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[8, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[8, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[8, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[8, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[8, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[8, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[8, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[8, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[8, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[8, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[8, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[8, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[8, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.core.seqgroup)": [[9, "ete4.core.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.__init__"]], "ete4.core.seqgroup": [[9, "module-ete4.core.seqgroup"]], "get_entries() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.get_entries"]], "get_seq() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.get_seq"]], "iter_entries() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.iter_entries"]], "set_seq() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.set_seq"]], "write() (seqgroup method)": [[9, "ete4.core.seqgroup.SeqGroup.write"]], "active (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.Active"]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace"]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.AlignedGrid"]], "alignmentface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AlignmentFace"]], "apptree (class in ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.AppTree"]], "arrowface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.ArrowFace"]], "attrface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.AttrFace"]], "box (class in ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.Box"]], "collapse_size (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE"]], "circleface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.CircleFace"]], "drawer (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.Drawer"]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces"]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces"]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc"]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces"]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerRect"]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces"]], "face (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.Face"]], "globalstuff (class in ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.GlobalStuff"]], "grid (class in ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.Grid"]], "htmlface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.HTMLFace"]], "imgface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.ImgFace"]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment"]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName"]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[10, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot"]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName"]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg"]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength"]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport"]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard"]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy"]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName"]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[10, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance"]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, 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"layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName"]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName"]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[10, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[10, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains"]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains"]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC"]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans"]], "legendface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.LegendFace"]], "min_size (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE"]], "npanels (drawer attribute)": [[10, "ete4.smartview.renderer.drawer.Drawer.NPANELS"]], "npanels (draweraligncircfaces attribute)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS"]], "npanels (draweralignrectfaces attribute)": [[10, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS"]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[10, "ete4.smartview.renderer.nodestyle.NodeStyle"]], "outlineface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.OutlineFace"]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.Padding"]], "piechartface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.PieChartFace"]], "rectface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.RectFace"]], "scaleface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.ScaleFace"]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.SelectedCircleFace"]], "selectedface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.SelectedFace"]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.SelectedRectFace"]], "seqface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.SeqFace"]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace"]], "size (class in ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.Size"]], "stackedbarface (class in 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"ete4.smartview.renderer.draw_helpers.circumasec"]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.circumrect"]], "clades (treeactive attribute)": [[10, "ete4.smartview.renderer.drawer.TreeActive.clades"]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.clip_angles"]], "compute_bounding_box() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box"]], "compute_bounding_box() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box"]], "compute_bounding_box() (circleface method)": [[10, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box"]], "compute_bounding_box() (face method)": [[10, "ete4.smartview.renderer.faces.Face.compute_bounding_box"]], "compute_bounding_box() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box"]], "compute_bounding_box() (rectface method)": [[10, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box"]], "compute_bounding_box() (scaleface method)": [[10, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box"]], "compute_bounding_box() (seqface method)": [[10, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box"]], "compute_bounding_box() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box"]], "compute_bounding_box() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box"]], "compute_fsize() (face method)": [[10, "ete4.smartview.renderer.faces.Face.compute_fsize"]], "compute_pie() (piechartface method)": [[10, "ete4.smartview.renderer.faces.PieChartFace.compute_pie"]], "content_size() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.content_size"]], "content_size() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.content_size"]], "copy_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.copy_style"]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.deactivate_clade"]], "deactivate_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.deactivate_node"]], "del_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.del_tree"]], "dist() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.dist"]], "draw() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.draw"]], "draw() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.draw"]], "draw() (arrowface method)": [[10, "ete4.smartview.renderer.faces.ArrowFace.draw"]], "draw() (circleface method)": [[10, "ete4.smartview.renderer.faces.CircleFace.draw"]], "draw() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw"]], "draw() (htmlface method)": [[10, "ete4.smartview.renderer.faces.HTMLFace.draw"]], "draw() (imgface method)": [[10, "ete4.smartview.renderer.faces.ImgFace.draw"]], "draw() (legendface method)": [[10, "ete4.smartview.renderer.faces.LegendFace.draw"]], "draw() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.draw"]], "draw() (piechartface method)": [[10, "ete4.smartview.renderer.faces.PieChartFace.draw"]], "draw() (rectface method)": [[10, "ete4.smartview.renderer.faces.RectFace.draw"]], "draw() (scaleface method)": [[10, "ete4.smartview.renderer.faces.ScaleFace.draw"]], "draw() (seqface method)": [[10, "ete4.smartview.renderer.faces.SeqFace.draw"]], "draw() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.draw"]], "draw() (stackedbarface method)": [[10, "ete4.smartview.renderer.faces.StackedBarFace.draw"]], "draw() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.draw"]], "draw_aligned_headers() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers"]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_arc"]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_array"]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_arrow"]], "draw_childrenline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline"]], "draw_childrenline() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline"]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_circle"]], "draw_collapsed() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed"]], "draw_collapsed() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed"]], "draw_collapsed() (drawercircfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed"]], "draw_collapsed() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed"]], "draw_collapsed() (drawerrectfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed"]], "draw_content() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_content"]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_ellipse"]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_html"]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_img"]], "draw_lengthline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline"]], "draw_lengthline() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline"]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_line"]], "draw_node() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.draw_node"]], "draw_node() (drawercircfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node"]], "draw_node() (drawerrectfaces method)": [[10, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node"]], "draw_nodebox() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox"]], "draw_nodebox() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox"]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_nodebox"]], "draw_nodedot() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot"]], "draw_nodedot() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot"]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_outline"]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_rect"]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_rhombus"]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_slice"]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_text"]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.draw_triangle"]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.drawn_size"]], "dx (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.dx"]], "dx (size attribute)": [[10, "ete4.smartview.renderer.drawer.Size.dx"]], "dy (box attribute)": [[10, "ete4.smartview.renderer.draw_helpers.Box.dy"]], "dy (size attribute)": [[10, "ete4.smartview.renderer.drawer.Size.dy"]], "ete4.smartview.gui.server": [[10, "module-ete4.smartview.gui.server"]], "ete4.smartview.renderer.draw_helpers": [[10, "module-ete4.smartview.renderer.draw_helpers"]], "ete4.smartview.renderer.drawer": [[10, "module-ete4.smartview.renderer.drawer"]], "ete4.smartview.renderer.face_positions": [[10, "module-ete4.smartview.renderer.face_positions"]], "ete4.smartview.renderer.faces": [[10, "module-ete4.smartview.renderer.faces"]], "ete4.smartview.renderer.layouts.context_layouts": [[10, "module-ete4.smartview.renderer.layouts.context_layouts"]], "ete4.smartview.renderer.layouts.default_layouts": [[10, "module-ete4.smartview.renderer.layouts.default_layouts"]], "ete4.smartview.renderer.layouts.domain_layouts": [[10, "module-ete4.smartview.renderer.layouts.domain_layouts"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[10, "module-ete4.smartview.renderer.layouts.eggnog6_layouts"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[10, "module-ete4.smartview.renderer.layouts.etecompare_layouts"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[10, "module-ete4.smartview.renderer.layouts.evocell_layouts"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[10, "module-ete4.smartview.renderer.layouts.evol_events_layouts"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[10, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[10, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[10, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[10, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[10, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[10, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[10, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[10, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[10, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[10, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[10, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[10, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[10, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[10, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [10, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[10, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[10, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[10, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[10, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_newick"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[10, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[10, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[10, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.include_props"]], "init() (nodestyle method)": [[10, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[10, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.json_error"]], "layouts (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[10, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.modify_tree_fields"]], "name (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[10, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[10, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[10, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.nodestyles"]], "on_first_visit() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[10, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[10, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[10, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[10, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[10, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[10, "ete4.smartview.gui.server.search_to_selection"]], "searches (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.searches"]], "selected (apptree attribute)": [[10, "ete4.smartview.gui.server.AppTree.selected"]], "selected_face (treestyle property)": [[10, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[10, 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"ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [10, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[10, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[10, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[10, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [10, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[10, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], 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"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"], [12, "faces"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [12, "nodestyle"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [12, "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"], [16, "taxonomy-databases"]], "NCBITaxa": [[10, "ncbitaxa"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "Tree (main class)": [[11, "tree-main-class"]], "Treeview (qt graphics)": [[12, "treeview-qt-graphics"]], "Tutorial": [[13, "tutorial"]], "Programmable tree drawing": [[14, "programmable-tree-drawing"]], "Overview": [[14, "overview"], [15, "overview"], [16, "overview"]], "Interactive visualization of trees": [[14, "interactive-visualization-of-trees"]], "Rendering trees as images": [[14, "rendering-trees-as-images"]], "Customizing the aspect of trees": [[14, "customizing-the-aspect-of-trees"]], "Tree style": [[14, "tree-style"]], "Show leaf node names, branch length and branch support": [[14, "show-leaf-node-names-branch-length-and-branch-support"]], "Change branch length scale (zoom in x)": [[14, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[14, "change-branch-separation-between-nodes-zoom-in-y"]], "Rotate a tree": [[14, "rotate-a-tree"]], "Circular tree in 180 degrees": [[14, "circular-tree-in-180-degrees"]], "Add legend and title": [[14, "add-legend-and-title"]], "Node style": [[14, "node-style"]], "Node faces": [[14, "node-faces"]], "Faces position": [[14, "faces-position"]], "Face properties": [[14, "face-properties"]], "Layout functions": [[14, "layout-functions"]], "Combining styles, faces and layouts": [[14, "combining-styles-faces-and-layouts"]], "Fixed node styles": [[14, "fixed-node-styles"]], "Node backgrounds": [[14, "node-backgrounds"]], "Img faces": [[14, "img-faces"]], "Bubble tree maps": [[14, "bubble-tree-maps"]], "Trees within trees": [[14, "trees-within-trees"]], "Phylogenetic trees and sequence domains": [[14, "phylogenetic-trees-and-sequence-domains"]], "Creating your custom interactive faces": [[14, "creating-your-custom-interactive-faces"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Implementation": [[15, "implementation"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[16, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[16, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Getting taxid information": [[16, "getting-taxid-information"]], "NCBI taxonomy": [[16, "ncbi-taxonomy"]], "GTDB taxonomy": [[16, "gtdb-taxonomy"]], "Getting descendant taxa": [[16, "getting-descendant-taxa"]], "Getting species tree topology": [[16, "getting-species-tree-topology"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[16, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "Working with the Tree structure": [[17, "working-with-the-tree-structure"]], "Trees": [[17, "trees"]], "Reading and writing newick trees": [[17, "reading-and-writing-newick-trees"]], "Creating a tree": [[17, "creating-a-tree"]], "Reading newick trees": [[17, "reading-newick-trees"]], "Writing newick trees": [[17, "writing-newick-trees"]], "Understanding ETE trees": [[17, "understanding-ete-trees"]], "Basic tree attributes": [[17, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[17, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[17, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[17, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[17, "traversing-browsing-trees"]], "Advanced traversing": [[17, "advanced-traversing"]], "Collapsing nodes while traversing": [[17, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[17, "iterators-or-lists"]], "Finding nodes by their properties": [[17, "finding-nodes-by-their-properties"]], "Search_all nodes matching a given criteria": [[17, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria (iteration)": [[17, "search-nodes-matching-a-given-criteria-iteration"]], "Find the first common ancestor": [[17, 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"ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__"]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__"]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__"]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__"]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__"]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__"]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__"]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__"]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__"]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__"]], "__init__() (seqface method)": [[9, 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(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, 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"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, 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"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, 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"ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts"]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle"]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle"]], "exclude_props (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.exclude_props"]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node"]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value"]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits"]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits"]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits"]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits"]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline"]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline"]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children"]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade"]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades"]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec"]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box"]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box"]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box"]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box"]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box"]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node"]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color"]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search"]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content"]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content"]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context"]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer"]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers"]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active"]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search"]], "get_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_fields"]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype"]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames"]], "get_layout_lca_rects() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_lca_rects"]], "get_layout_ogs_egg5() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_ogs_egg5"]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname"]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts"]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters"]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend"]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type"]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick"]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info"]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline"]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents"]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser"]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props"]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect"]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function"]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children"]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info"]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections"]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq"]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq"]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats"]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid"]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip"]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search"]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file"]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form"]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick"]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs"]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys"]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport"]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport"]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport"]], "include_props (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.include_props"]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init"]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize"]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style"]], "initialized (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.initialized"]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles"]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box"]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment"]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed"]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small"]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small"]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error"]], "layouts (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.layouts"]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree"]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick"]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance"]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box"]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces"]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name"]], "modify_tree_fields() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.modify_tree_fields"]], "name (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.name"]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html"]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size"]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size"]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes"]], "nodestyles (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.nodestyles"]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit"]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit"]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window"]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation"]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents"]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection"]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active"]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade"]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search"]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection"]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json"]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results"]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts"]], "retrieve_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree"]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview"]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string"]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval"]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection"]], "searches (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.searches"]], "selected (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.selected"]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face"]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos"]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style"]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style"]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style"]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style"]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style"]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style"]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style"]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style"]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style"]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style"], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style"]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style"]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style"]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style"]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style"]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style"]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style"]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style"]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style"]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style"]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style"]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style"]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style"], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style"]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style"]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style"]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort"]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis"]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack"]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active"]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search"]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection"]], "style (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.style"]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary"]], "timer (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.timer"]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get"]], "tree (apptree attribute)": [[9, "ete4.smartview.gui.server.AppTree.tree"]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node"]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts"]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts"]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props"]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style"]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection"]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x"]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x"]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y"]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y"]], "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"]], "phonehome() (tree method)": [[11, "ete4.Tree.phonehome"]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child"]], "populate() (tree method)": [[11, "ete4.Tree.populate"]], "props (tree attribute)": [[11, "ete4.Tree.props"]], "prune() (tree method)": [[11, "ete4.Tree.prune"]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child"]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children"]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister"]], "render() (tree method)": [[11, "ete4.Tree.render"]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy"]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children"]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds"]], "root (tree attribute)": [[11, "ete4.Tree.root"]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors"]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants"]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name"]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes"]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup"]], "set_style() (tree method)": [[11, "ete4.Tree.set_style"]], "show() (tree method)": [[11, "ete4.Tree.show"]], "size (tree attribute)": [[11, "ete4.Tree.size"]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style"]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants"]], "standardize() (tree method)": [[11, "ete4.Tree.standardize"]], "support (tree attribute)": [[11, "ete4.Tree.support"]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children"]], "to_str() (tree method)": [[11, "ete4.Tree.to_str"]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric"]], "traverse() (tree method)": [[11, "ete4.Tree.traverse"]], "unroot() (tree method)": [[11, "ete4.Tree.unroot"]], "up (tree attribute)": [[11, "ete4.Tree.up"]], "write() (tree method)": [[11, "ete4.Tree.write"]], "treeview": [[12, "module-treeview"]]}})
\ No newline at end of file
diff --git a/tutorial/index.html b/tutorial/index.html
index c20a57f62..a93e8e046 100644
--- a/tutorial/index.html
+++ b/tutorial/index.html
@@ -77,6 +77,16 @@ 
    Tutorial
 
  • Combining styles, faces and layouts
    • 
 
 
+
  • Taxonomy databases
+
    • 
 
 
    
 
@@ -106,6 +116,7 @@ 
    Navigation
    
 
  • Working with the Tree structure
    • 
 
  • Phylogenetic trees
    • 
 
  • Programmable tree drawing
    • 
+
  • Taxonomy databases
    • 
 
 
 
  • Reference Guide
    • 
diff --git a/tutorial/tutorial_drawing.html b/tutorial/tutorial_drawing.html
index a08048d33..1e587a2c4 100644
--- a/tutorial/tutorial_drawing.html
+++ b/tutorial/tutorial_drawing.html
@@ -15,7 +15,7 @@
     
     
     
-    
+    
     
    
   
@@ -1153,6 +1153,7 @@ 
    Navigation
    
 
  • Working with the Tree structure
    • 
 
  • Phylogenetic trees
    • 
 
  • Programmable tree drawing
    • 
+
  • Taxonomy databases
    • 
 
 
 
  • Reference Guide
    • 
@@ -1164,7 +1165,7 @@ 
    Related Topics
    
   
  • Documentation overview
    • 
 
diff --git a/tutorial/tutorial_phylogeny.html b/tutorial/tutorial_phylogeny.html
index 0dbcb602e..97b212c60 100644
--- a/tutorial/tutorial_phylogeny.html
+++ b/tutorial/tutorial_phylogeny.html
@@ -1022,6 +1022,7 @@ 
    Navigation
    
 
  • Working with the Tree structure
    • 
 
  • Phylogenetic trees
    • 
 
  • Programmable tree drawing
    • 
+
  • Taxonomy databases
    • 
 
 
 
  • Reference Guide
    • 
diff --git a/tutorial/tutorial_taxonomy.html b/tutorial/tutorial_taxonomy.html
index 69eed166b..c7b5d9d0d 100644
--- a/tutorial/tutorial_taxonomy.html
+++ b/tutorial/tutorial_taxonomy.html
@@ -5,7 +5,7 @@
     
     
 
-    Connecting with Taxonomy Databases — ETE Toolkit 4.0.0-beta documentation
+    Taxonomy databases — ETE Toolkit 4.0.0-beta documentation
     
     
     
@@ -15,6 +15,8 @@
     
     
     
+    
+    
    
   
   
@@ -31,154 +33,188 @@
 
           
    
             
-  
    
-
    Connecting with Taxonomy Databases
    
+  
    
+
    Taxonomy databases
    
 
 
    
-
    Overview
    
-
    ETE4 contains ncbi_taxonomy and gtdb_taxonomy modules which provide
-utilities to efficiently query a local copy of the NCBI or GTDB taxonomy
-databases. The class NCBITaxa and GTDBTaxa offer methods to convert
-from taxid to names (and vice versa), to fetch pruned topologies connecting
-a given set of species, or to download rank, names and lineage track information.
    
-
    It is also fully integrated with PhyloTree instances through the
-PhyloNode.annotate_ncbi_taxa() and ``PhyloNode.annotate_gtdb_taxa()``method.
    
+
    Overview
    
+
    ETE4 contains the ncbi_taxonomy and gtdb_taxonomy modules which
+provide utilities to efficiently query a local copy of the NCBI or
+GTDB taxonomy databases. The classes NCBITaxa and
+GTDBTaxa offer methods to convert from taxid to names (and
+vice versa), to fetch pruned topologies connecting a given set of
+species, or to download rank, names and lineage track information.
    
+
    It is also fully integrated with PhyloTree instances through
+the annotate_ncbi_taxa() and
+annotate_gtdb_taxa() methods.
    
 
    
 
    
-
    Differences between NCBI and GTDB taxonomies in ETE4
    
-
    The NCBI taxonomy database is a comprehensive resource for organism names and
-classifications.It is updated daily and offers multiple access points including a web
-portal, an FTP server. The database releases its data in a package called “taxdump.tar.gz” which
-contains several .dmp files.
    
-
    Taxon in NCBI taxonomyis usually a numeric identifier, commonly representing
-taxa (“TaxID”), but it can also signify other entities like genetic codes or citations, such as
-9606 represents Homo Sapiens.
    
-
    On the other hand, GTDB taxonomy is distributed as simple text files, uses a genome-based
-approach for classification, and the identifiers are usually specific to genomes rather
-than taxa.
    
-
    Since ETE Toolkit version 3, ete3 parses taxdump file to local sqlite database to fullfill the
-methods in ncbi_taxonomy module. We applied the same strategy to GTDBTaxa. While the original GTDB
-taxonomy data differs from NCBI taxonomy files, a conversion step is essential for integration.
    
-
    To integrate GTDB into the ETE Toolkit v4, a conversion process was necessary. A third-party script
-(https://github.com/nick-youngblut/gtdb_to_taxdump) was employed to convert the GTDB taxonomy to the
-NCBI-like taxdump format. We already preprared GTDB taxonomy dump file from different releases version
-and store in https://github.com/etetoolkit/ete-data/tree/main/gtdb_taxonomy.
    
+
    Differences between NCBI and GTDB taxonomies in ETE4
    
+
    The NCBI taxonomy database is a comprehensive resource for organism
+names and classifications.It is updated daily and offers multiple
+access points including a web portal, an FTP server. The database
+releases its data in a package called “taxdump.tar.gz” which contains
+several .dmp files.
    
+
    Taxon in NCBI taxonomyis usually a numeric identifier, commonly
+representing taxa (“TaxID”), but it can also signify other entities
+like genetic codes or citations, such as 9606 represents Homo Sapiens.
    
+
    On the other hand, GTDB taxonomy is distributed as simple text files,
+uses a genome-based approach for classification, and the identifiers
+are usually specific to genomes rather than taxa.
    
+
    Since ETE Toolkit version 3, ETE parses taxdump file and stores it in
+a local sqlite database to fullfill the methods in ncbi_taxonomy
+module. We applied the same strategy to GTDBTaxa. While the original
+GTDB taxonomy data differs from NCBI taxonomy files, a conversion step
+is essential for integration.
    
+
    To integrate GTDB into the ETE Toolkit v4, a conversion process is
+necessary. A third-party script
+(https://github.com/nick-youngblut/gtdb_to_taxdump) is employed to
+convert the GTDB taxonomy to the NCBI-like taxdump format. We already
+preprared GTDB taxonomy dump file from different releases version and
+store in
+https://github.com/etetoolkit/ete-data/tree/main/gtdb_taxonomy.
    
 
    
 
    
-
    Setting up local copies of the NCBI and GTDB taxonomy databases
    
-
    The first time you attempt to use NCBITaxa or GTDBTaxa, ETE will detect that your local
-database is empty and it will attempt to download the latest taxonomy database(NCBI ~600MB;GTDB ~72MB) and will
-store a parsed version of it in your home directory: ~/.local/share/ete/.
-All future imports of NCBITaxa or GTDBTaxa will detect the local database and will
-skip this step.
    
-
    
-
    Example::
    # Load NCBI module
-from ete4 import NCBITaxa
-ncbi = NCBITaxa()
-ncbi.update_taxonomy_database()
    
-
    # Load GTDB module
-from ete4 import GTDBTaxa
-gtdb = GTDBTaxa()
-gtdb.update_taxonomy_database()
    
-
    # Load GTDB module with specific release version
-from ete4 import GTDBTaxa
-gtdb = GTDBTaxa()
    
-
    # latest release updated in https://github.com/dengzq1234/ete-data/tree/main/gtdb_taxonomy
-gtdb.update_taxonomy_database()
-# or
-gtdb.update_taxonomy_database(“gtdbdump.tar.gz”)
    
-
    # update with custom release 202
-gtdb.update_taxonomy_database(‘gtdb202dump.tar.gz’)
    
-
    
-
    
+
    Setting up local copies of the NCBI and GTDB taxonomy databases
    
+
    The first time you attempt to use NCBITaxa or GTDBTaxa, ETE will
+detect that your local database is empty and will attempt to download
+the latest taxonomy database (NCBI ~600MB, GTDB ~72MB) and will store
+a parsed version of it in ~/.local/share/ete/ by default. All future
+imports of NCBITaxa or GTDBTaxa will detect the local database and
+will skip this step.
    
+
    Example:
    
+
    # Load NCBI module
+from ete4 import NCBITaxa
+ncbi = NCBITaxa()
+ncbi.update_taxonomy_database()
+
+# Load GTDB module
+from ete4 import GTDBTaxa
+gtdb = GTDBTaxa()
+gtdb.update_taxonomy_database()
+
+# Load GTDB module with specific release version
+from ete4 import GTDBTaxa
+gtdb = GTDBTaxa()
+
+# latest release updated in https://github.com/dengzq1234/ete-data/tree/main/gtdb_taxonomy
+gtdb.update_taxonomy_database()
+# or
+gtdb.update_taxonomy_database("gtdbdump.tar.gz")
+
+# update with custom release 202
+gtdb.update_taxonomy_database('gtdb202dump.tar.gz')
+
    
+
    
 
    
 
    
-
    Getting taxid information
    
+
    Getting taxid information
    
 
    
-
    NCBI taxonomy
    
-
    you can fetch species names, ranks and linage track information for your taxids using the following
-methods:
    
-
      
-
    • NCBITaxa.get_rank()
      • 
-
    • NCBITaxa.get_lineage()
      • 
-
    • NCBITaxa.get_taxid_translator()
      • 
-
    • NCBITaxa.get_name_translator()
      • 
-
    • NCBITaxa.translate_to_names()
      • 
-
    
-
    The so called get-translator-functions will return a dictionary converting between taxids and species names.
-Either species or linage names/taxids are accepted as input.
    
-
    
-
    Example::
    from ete4 import NCBITaxa
-ncbi = NCBITaxa()
-taxid2name = ncbi.get_taxid_translator([9606, 9443])
-print(taxid2name)
-# {9443: ‘Primates’, 9606: ‘Homo sapiens’}
    
-
    name2taxid = ncbi.get_name_translator([‘Homo sapiens’, ‘primates’])
-print(name2taxid)
-# {‘Homo sapiens’: [9606], ‘primates’: [9443]}
    
-
    # when the same name points to several taxa, all taxids are returned
-name2taxid = ncbi.get_name_translator([‘Bacteria’])
-print(name2taxid)
-# {‘Bacteria’: [2, 629395]}
    
-
    
-
    
-
    Other functions allow to extract further information using taxid numbers as a query.
    
-
    
-
    Example::
    from ete4 import NCBITaxa
-ncbi = NCBITaxa()
    
-
    print(ncbi.get_rank([9606, 9443]))
-# {9443: u’order’, 9606: u’species’}
    
-
    print(ncbi.get_lineage(9606))
-# [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
-# 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
-# 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
-# 9606]
    
-
    
-
    
-
    Combine combine all at once:
    
-
    
-
    Example::
    from ete4 import NCBITaxa
-ncbi = NCBITaxa()
    
-
    lineage = ncbi.get_lineage(9606)
-print(lineage)
    
-
    # [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
-# 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
-# 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
-# 9606]
    
-
    names = ncbi.get_taxid_translator(lineage)
-print([names[taxid] for taxid in lineage])
    
-
    # [u’root’, u’cellular organisms’, u’Eukaryota’, u’Opisthokonta’, u’Metazoa’,
-# u’Eumetazoa’, u’Bilateria’, u’Deuterostomia’, u’Chordata’, u’Craniata’,
-# u’Vertebrata’, u’Gnathostomata’, u’Teleostomi’, u’Euteleostomi’,
-# u’Sarcopterygii’, u’Dipnotetrapodomorpha’, u’Tetrapoda’, u’Amniota’,
-# u’Mammalia’, u’Theria’, u’Eutheria’, u’Boreoeutheria’, u’Euarchontoglires’,
-# u’Primates’, u’Haplorrhini’, u’Simiiformes’, u’Catarrhini’, u’Hominoidea’,
-# u’Hominidae’, u’Homininae’, u’Homo’, u’Homo sapiens’]
    
-
    
-
    
+
    NCBI taxonomy
    
+
    You can fetch species names, ranks and linage track information for
+your taxids using the following methods:
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NCBITaxa.get_rank(taxids)
    Return dict with NCBI taxonomy ranks for each list of taxids.
    NCBITaxa.get_lineage(taxid)
    Return lineage track corresponding to the given taxid.
    NCBITaxa.get_taxid_translator(taxids[, ...])
    Return dict with the scientific names corresponding to the taxids.
    NCBITaxa.get_name_translator(names)
    Return dict with taxids corresponding to the given scientific names.
    NCBITaxa.translate_to_names(taxids)
    Return list of scientific names corresponding to taxids.
    
+
    The so called get-translator functions will return a dictionary
+converting between taxids and species names. Either species or linage
+names/taxids are accepted as input.
    
+
    Example:
    
+
    from ete4 import NCBITaxa
+ncbi = NCBITaxa()
+taxid2name = ncbi.get_taxid_translator([9606, 9443])
+print(taxid2name)
+# {9443: 'Primates', 9606: 'Homo sapiens'}
+
+name2taxid = ncbi.get_name_translator(['Homo sapiens', 'primates'])
+print(name2taxid)
+# {'Homo sapiens': [9606], 'primates': [9443]}
+
+# when the same name points to several taxa, all taxids are returned
+name2taxid = ncbi.get_name_translator(['Bacteria'])
+print(name2taxid)
+# {'Bacteria': [2, 629395]}
+
    
+
    
+
    Other functions allow to extract further information using taxid
+numbers as a query.
    
+
    Example:
    
+
    from ete4 import NCBITaxa
+ncbi = NCBITaxa()
+
+print(ncbi.get_rank([9606, 9443]))
+# {9443: 'order', 9606: 'species'}
+
+print(ncbi.get_lineage(9606))
+# [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
+# 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
+# 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
+# 9606]
+
    
+
    
+
    Example combining all at once:
    
+
    from ete4 import NCBITaxa
+ncbi = NCBITaxa()
+
+lineage = ncbi.get_lineage(9606)
+print(lineage)
+
+# [1, 131567, 2759, 33154, 33208, 6072, 33213, 33511, 7711, 89593, 7742,
+# 7776, 117570, 117571, 8287, 1338369, 32523, 32524, 40674, 32525, 9347,
+# 1437010, 314146, 9443, 376913, 314293, 9526, 314295, 9604, 207598, 9605,
+# 9606]
+
+names = ncbi.get_taxid_translator(lineage)
+print([names[taxid] for taxid in lineage])
+
+# ['root', 'cellular organisms', 'Eukaryota', 'Opisthokonta', 'Metazoa',
+# 'Eumetazoa', 'Bilateria', 'Deuterostomia', 'Chordata', 'Craniata',
+# 'Vertebrata', 'Gnathostomata', 'Teleostomi', 'Euteleostomi',
+# 'Sarcopterygii', 'Dipnotetrapodomorpha', 'Tetrapoda', 'Amniota',
+# 'Mammalia', 'Theria', 'Eutheria', 'Boreoeutheria', 'Euarchontoglires',
+# 'Primates', 'Haplorrhini', 'Simiiformes', 'Catarrhini', 'Hominoidea',
+# 'Hominidae', 'Homininae', 'Homo', 'Homo sapiens']
+
    
+
    
 
    
 
    
-
    GTDB taxonomy
    
+
    GTDB taxonomy
    
 
    In the NCBI taxonomy database, each species is assigned a unique numeric taxid.
 For example, the taxid 9606 refers to Homo sapiens. These taxids serve as
 essential keys for tracking lineages within the database.
    
@@ -189,192 +225,186 @@ 
    GTDB taxonomy
 
    Like NCBITaxa, GTDBTaxa contains similar methods:
    
-
      
-
    • GTDBTaxa.get_rank()
      • 
-
    • GTDBTaxa.get_lineage()
      • 
-
    • GTDBTaxa.get_taxid_translator()
      • 
-
    • GTDBTaxa.get_name_translator()
      • 
-
    • GTDBTaxa.translate_to_names()
      • 
-
    • GTDBTaxa.get_name_lineage()
      • 
-
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    GTDBTaxa.get_rank(taxids)
    Return dictionary converting taxids to their GTDB taxonomy rank.
    GTDBTaxa.get_lineage(taxid)
    Given a valid taxid number, return its corresponding lineage track as a hierarchically sorted list of parent taxids.
    GTDBTaxa.get_taxid_translator(taxids[, ...])
    Given a list of taxids, returns a dictionary with their corresponding scientific names.
    GTDBTaxa.get_name_translator(names)
    Given a list of taxid scientific names, returns a dictionary translating them into their corresponding taxids.
    GTDBTaxa.translate_to_names(taxids)
    Given a list of taxid numbers, returns another list with their corresponding scientific names.
    GTDBTaxa.get_name_lineage(taxnames)
    Given a valid taxname, return its corresponding lineage track as a hierarchically sorted list of parent taxnames.
    
 
    
 
    
 
    
-
    Getting descendant taxa
    
+
    Getting descendant taxa
    
 
    Given a taxid or a taxa name from an internal node in the NCBI/GTDB taxonomy tree,
 their descendants can be retrieved as follows:
    
-
    NCBI taxonomy
-Example:
    
-
    # example in NCBI taxonomy
-from ete4 import NCBITaxa
+
    NCBI taxonomy example:
    
+
    from ete4 import NCBITaxa
 ncbi = NCBITaxa()
 
 descendants = ncbi.get_descendant_taxa('Homo')
 print(ncbi.translate_to_names(descendants))
 
-# [u'Homo heidelbergensis', u'Homo sapiens ssp. Denisova',
-# u'Homo sapiens neanderthalensis']
+# ['Homo heidelbergensis', 'Homo sapiens ssp. Denisova',
+# 'Homo sapiens neanderthalensis']
 
-# you can easily ignore subspecies, so only taxa labeled as "species" will be reported:
+# You can easily ignore subspecies, so only taxa labeled as "species" will be reported:
 descendants = ncbi.get_descendant_taxa('Homo', collapse_subspecies=True)
 print(ncbi.translate_to_names(descendants))
 
-# [u'Homo sapiens', u'Homo heidelbergensis']
+# ['Homo sapiens', 'Homo heidelbergensis']
 
 # or even returned as an annotated tree
 tree = ncbi.get_descendant_taxa('Homo', collapse_subspecies=True, return_tree=True)
 
 print(tree.to_str(props=['sci_name','taxid']))
-
-"""
-           ╭╴environmental samples,2665952╶╌╴Homo sapiens environmental sample,2665953
-           │
-           ├╴Homo sapiens,9606
-╴Homo,9605╶┤
-           ├╴Homo heidelbergensis,1425170
-           │
-           ╰╴unclassified Homo,2813598╶╌╴Homo sp.,2813599
-"""
+#            ╭╴environmental samples,2665952╶╌╴Homo sapiens environmental sample,2665953
+#            │
+#            ├╴Homo sapiens,9606
+# ╴Homo,9605╶┤
+#            ├╴Homo heidelbergensis,1425170
+#            │
+#            ╰╴unclassified Homo,2813598╶╌╴Homo sp.,2813599
 
    
 
    
-
    GTDB taxonomy
-Example:
    
+
    GTDB taxonomy example:
    
 
    from ete4 import GTDBTaxa
 gtdb = GTDBTaxa()
 descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae')
 print(descendants)
-# ['GB_GCA_003662765.1', 'GB_GCA_003662805.1', 'GB_GCA_003345555.1', 'GB_GCA_003345595.1', 'GB_GCA_001940705.1', 'GB_GCA_001563335.1', 'GB_GCA_011364905.1', 'GB_GCA_004376265.1', 'GB_GCA_002825515.1', 'GB_GCA_001563325.1', 'GB_GCA_011364985.1', 'GB_GCA_011365025.1', 'GB_GCA_004524565.1', 'GB_GCA_004524595.1', 'GB_GCA_002825465.1', 'GB_GCA_002825535.1', 'GB_GCA_003345545.1', 'GB_GCA_004524445.1', 'GB_GCA_013388835.1', 'GB_GCA_008080745.1', 'GB_GCA_004524435.1', 'GB_GCA_013138615.1']
+# ['GB_GCA_003662765.1', 'GB_GCA_003662805.1', ..., 'GB_GCA_013138615.1']
 
-#ignore subspecies, so only taxa labeled as "species" will be reported
+# Ignore subspecies, so only taxa labeled as "species" will be reported.
 descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae', collapse_subspecies=True)
-
 print(descendants)
+# ['s__MP8T-1 sp002825535', 's__MP8T-1 sp003345545', ..., 's__TEKIR-12S sp004524435']
 
-#['s__MP8T-1 sp002825535', 's__MP8T-1 sp003345545', 's__MP8T-1 sp002825465', 's__MP8T-1 sp004524565', 's__MP8T-1 sp004524595', 's__SMTZ1-83 sp011364985', 's__SMTZ1-83 sp011365025', 's__SMTZ1-83 sp001563325', 's__TEKIR-14 sp004524445', 's__SHMX01 sp008080745', 's__OWC5 sp003345595', 's__OWC5 sp003345555', 's__JACAEL01 sp013388835', 's__B65-G9 sp003662765', 's__SMTZ1-45 sp001563335', 's__SMTZ1-45 sp011364905', 's__SMTZ1-45 sp001940705', 's__SMTZ1-45 sp004376265', 's__SMTZ1-45 sp002825515', 's__WTCK01 sp013138615', 's__TEKIR-12S sp004524435']
-
-
-#returned as an annotated tree
+# Returned as an annotated tree.
 descendants = gtdb.get_descendant_taxa('f__Thorarchaeaceae', collapse_subspecies=True, return_tree=True)
 print(descendants.to_str(props=['sci_name','rank']))
-"""
-                                            ╭╴s__MP8T-1 sp002825535,species
-                                            │
-                                            ├╴s__MP8T-1 sp003345545,species
-                                            │
-                        ╭╴g__MP8T-1,genus╶┼╴s__MP8T-1 sp002825465,species
-                        │                 │
-                        │                 ├╴s__MP8T-1 sp004524565,species
-                        │                 │
-                        │                 ╰╴s__MP8T-1 sp004524595,species
-                        │
-                        │                   ╭╴s__SMTZ1-83 sp011364985,species
-                        │                   │
-                        ├╴g__SMTZ1-83,genus╶┼╴s__SMTZ1-83 sp011365025,species
-                        │                   │
-                        │                   ╰╴s__SMTZ1-83 sp001563325,species
-                        │
-                        ├╴g__TEKIR-14,genus╶╌╴s__TEKIR-14 sp004524445,species
-                        │
-                        ├╴g__SHMX01,genus╶╌╴s__SHMX01 sp008080745,species
-                        │
-                        │               ╭╴s__OWC5 sp003345595,species
-                        ├╴g__OWC5,genus╶┤
-╴f__Thorarchaeaceae,family╶┤               ╰╴s__OWC5 sp003345555,species
-                        │
-                        ├╴g__JACAEL01,genus╶╌╴s__JACAEL01 sp013388835,species
-                        │
-                        ├╴g__B65-G9,genus╶╌╴s__B65-G9 sp003662765,species
-                        │
-                        │                   ╭╴s__SMTZ1-45 sp001563335,species
-                        │                   │
-                        │                   ├╴s__SMTZ1-45 sp011364905,species
-                        │                   │
-                        ├╴g__SMTZ1-45,genus╶┼╴s__SMTZ1-45 sp001940705,species
-                        │                   │
-                        │                   ├╴s__SMTZ1-45 sp004376265,species
-                        │                   │
-                        │                   ╰╴s__SMTZ1-45 sp002825515,species
-                        │
-                        ├╴g__WTCK01,genus╶╌╴s__WTCK01 sp013138615,species
-                        │
-                        ╰╴g__TEKIR-12S,genus╶╌╴s__TEKIR-12S sp004524435,species
-"""
+#                                ╭╴s__MP8T-1 sp002825535,species
+#                                │
+#                                ├╴s__MP8T-1 sp003345545,species
+#                                │
+#              ╭╴g__MP8T-1,genus╶┼╴s__MP8T-1 sp002825465,species
+#              │                 │
+#              │                 ├╴s__MP8T-1 sp004524565,species
+#              │                 │
+#              │                 ╰╴s__MP8T-1 sp004524595,species
+#              │
+#              │                   ╭╴s__SMTZ1-83 sp011364985,species
+#              │                   │
+#              ├╴g__SMTZ1-83,genus╶┼╴s__SMTZ1-83 sp011365025,species
+#              │                   │
+#              │                   ╰╴s__SMTZ1-83 sp001563325,species
+#              │
+#              ├╴g__TEKIR-14,genus╶╌╴s__TEKIR-14 sp004524445,species
+#              │
+#              ├╴g__SHMX01,genus╶╌╴s__SHMX01 sp008080745,species
+#              │
+#              │               ╭╴s__OWC5 sp003345595,species
+#              ├╴g__OWC5,genus╶┤
+# ╴f__Tho[...]╶┤               ╰╴s__OWC5 sp003345555,species
+#              │
+#              ├╴g__JACAEL01,genus╶╌╴s__JACAEL01 sp013388835,species
+#              │
+#              ├╴g__B65-G9,genus╶╌╴s__B65-G9 sp003662765,species
+#              │
+#              │                   ╭╴s__SMTZ1-45 sp001563335,species
+#              │                   │
+#              │                   ├╴s__SMTZ1-45 sp011364905,species
+#              │                   │
+#              ├╴g__SMTZ1-45,genus╶┼╴s__SMTZ1-45 sp001940705,species
+#              │                   │
+#              │                   ├╴s__SMTZ1-45 sp004376265,species
+#              │                   │
+#              │                   ╰╴s__SMTZ1-45 sp002825515,species
+#              │
+#              ├╴g__WTCK01,genus╶╌╴s__WTCK01 sp013138615,species
+#              │
+#              ╰╴g__TEKIR-12S,genus╶╌╴s__TEKIR-12S sp004524435,species
 
    
 
    
 
    
 
    
-
    Getting species tree topology
    
-
    Getting the taxonomy tree for a given set of species is one of the most useful ways
-to get all information at once. The method NCBITaxa.get_topology() or GTDBTaxa.get_topology() allows to query your
-local NCBI/GTDB database and extract the smallest tree that connects all your query taxids.
-It returns a normal ETE tree in which all nodes, internal or leaves, are annotated for
-lineage, scientific names, ranks, and so on.
    
-
    NCBI taxonomy
-Example:
    
+
    Getting species tree topology
    
+
    Getting the taxonomy tree for a given set of species is one of the
+most useful ways to get all information at once. The methods
+NCBITaxa.get_topology() or GTDBTaxa.get_topology() allow
+to query your local NCBI/GTDB database and extract the smallest tree
+that connects all your query taxids. It returns a normal ETE tree in
+which all nodes, internal or leaves, are annotated for lineage,
+scientific names, ranks, and so on.
    
+
    NCBI taxonomy example:
    
 
    from ete4 import NCBITaxa
 ncbi = NCBITaxa()
 
 tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
 
 print(tree.to_str(props=["sci_name", "rank"]))
-"""
-                    ╭╴Dendrochirotida,order
-                    │
-                    │                                                                   ╭╴Homo sapiens,species
-╴Deuterostomia,clade╶┤                                             ╭╴Homininae,subfamily╶┤
-                    │               ╭╴Euarchontoglires,superorder╶┤                     ╰╴Pan troglodytes,species
-                    │               │                             │
-                    ╰╴Amniota,clade╶┤                             ╰╴Mus musculus,species
-                                    │
-                                    ╰╴Aves,class
-"""
-
-# all intermediate nodes connecting the species can also be kept in the tree
+#                      ╭╴Dendrochirotida,order
+#                      │
+#                      │                                                                   ╭╴Homo sapiens,species
+# ╴Deuterostomia,clade╶┤                                             ╭╴Homininae,subfamily╶┤
+#                      │               ╭╴Euarchontoglires,superorder╶┤                     ╰╴Pan troglodytes,species
+#                      │               │                             │
+#                      ╰╴Amniota,clade╶┤                             ╰╴Mus musculus,species
+#                                      │
+#                                      ╰╴Aves,class
+
+# All intermediate nodes connecting the species can also be kept in the tree.
 tree = ncbi.get_topology([2, 33208], intermediate_nodes=True)
 print(tree.to_str(props=["sci_name"]))
-"""
-                    ╭╴Eukaryota╶╌╴Opisthokonta╶╌╴Metazoa
-╴cellular organisms╶┤
-                    ╰╴Bacteria
-"""
+#                     ╭╴Eukaryota╶╌╴Opisthokonta╶╌╴Metazoa
+# ╴cellular organisms╶┤
+#                     ╰╴Bacteria
 
    
 
    
-
    GTDB taxonomy
-Example:
    
+
    GTDB taxonomy example:
    
 
    from ete4 import GTDBTaxa
 gtdb = GTDBTaxa()
 
 tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae"])
 print(tree.to_str(props=['sci_name', 'rank']))
+#                                         ╭╴p__Huberarchaeota,phylum
+#               ╭╴d__Archaea,superkingdom╶┤
+# ╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
+#               │
+#               ╰╴o__Peptococcales,order
 
-"""
-                                        ╭╴p__Huberarchaeota,phylum
-            ╭╴d__Archaea,superkingdom╶┤
-╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
-            │
-            ╰╴o__Peptococcales,order
-
-"""
-
-# all intermediate nodes connecting the species can also be kept in the tree
+# All intermediate nodes connecting the species can also be kept in the tree.
 tree = gtdb.get_topology(["p__Huberarchaeota", "o__Peptococcales", "f__Korarchaeaceae"], intermediate_nodes=True, collapse_subspecies=True, annotate=True)
 print(tree.to_str(props=['sci_name', 'rank']))
-"""
-                                        ╭╴p__Huberarchaeota,phylum
-            ╭╴d__Archaea,superkingdom╶┤
-╴root,no rank╶┤                         ╰╴p__Thermoproteota,phylum╶╌╴c__Korarchaeia,class╶╌╴o__Korarchaeales,order╶╌╴f__Korarchaeaceae,family
-            │
-            ╰╴d__Bacteria,superkingdom╶╌╴p__Firmicutes_B,phylum╶╌╴c__Peptococcia,class╶╌╴o__Peptococcales,order
-"""
+#                                         ╭╴p__Huberarchaeota,phylum
+#               ╭╴d__Archaea,superkingdom╶┤
+# ╴root,no rank╶┤                         ╰╴p__Thermoproteota,phylum╶╌╴c__Korarchaeia,class╶╌╴o__Korarchaeales,order╶╌╴f__Korarchaeaceae,family
+#               │
+#               ╰╴d__Bacteria,superkingdom╶╌╴p__Firmicutes_B,phylum╶╌╴c__Peptococcia,class╶╌╴o__Peptococcales,order
 
    
 
    
 
    
 
    
-
    Automatic tree annotation using NCBI/GTDB taxonomy
    
-
    NCBI/GTDB taxonomy annotation consists of adding additional information to any internal a leaf node
-in a give user tree. Only an property containing the taxid associated to each node
-is required for the nodes in the query tree. The annotation process will add the
-following features to the nodes:
    
+
    Automatic tree annotation using NCBI/GTDB taxonomy
    
+
    NCBI/GTDB taxonomy annotation consists of adding additional
+information to any internal or leaf node in a tree. Only a property
+containing the taxid associated to each node is required for the nodes
+in the query tree. The annotation process will add the following
+features to the nodes:
    
 
-
    Note that, for internal nodes, taxid can be automatically inferred based on their sibling
-nodes. The easiest way to annotate a tree is to use a PhyloTree instance where the species
-name attribute is transparently used as the taxid attribute. Note that
-the :PhyloNode:`annotate_ncbi_taxa`: or :PhyloNode:`annotate_gtdb_taxa`: function will also return the used name, lineage and
-rank translators.
    
-
    Remember that species names in PhyloTree instances are automatically extracted from leaf names. The parsing method can be easily adapted to any formatting:
    
-
    NCBI taxonomy
-Example:
    
+
    Note that, for internal nodes, taxid can be automatically inferred
+based on their sibling nodes. The easiest way to annotate a tree is to
+use a PhyloTree instance where the species name attribute is
+transparently used as the taxid attribute. Note that the
+annotate_ncbi_taxa() or
+annotate_gtdb_taxa() function will also return the
+used name, lineage and rank translators.
    
+
    Remember that species names in PhyloTree instances are automatically
+extracted from leaf names. The parsing method can be easily adapted to
+any formatting:
    
+
    NCBI taxonomy example:
    
 
    from ete4 import PhyloTree
 
-# load the whole leaf name as species taxid
+# Load the whole leaf name as species taxid.
 tree = PhyloTree('((9606, 9598), 10090);', sp_naming_function=lambda name: name)
 tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
 
-
-# split names by '|' and return the first part as the species taxid
+# Split names by '|' and return the first part as the species taxid.
 tree = PhyloTree('((9606|protA, 9598|protA), 10090|protB);', sp_naming_function=lambda name: name.split('|')[0])
 tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa()
 
 print(tree.to_str(props=["name", "sci_name", "taxid"]))
-
-"""
-                                                            ╭╴9606|protA,Homo sapiens,9606
-                                 ╭╴(empty),Homininae,207598╶┤
-╴(empty),Euarchontoglires,314146╶┤                          ╰╴9598|protA,Pan troglodytes,9598
-                                 │
-                                 ╰╴10090|protB,Mus musculus,10090
-"""
+#                                                             ╭╴9606|protA,Homo sapiens,9606
+#                                  ╭╴(empty),Homininae,207598╶┤
+# ╴(empty),Euarchontoglires,314146╶┤                          ╰╴9598|protA,Pan troglodytes,9598
+#                                  │
+#                                  ╰╴10090|protB,Mus musculus,10090
 
    
 
    
-
    GTDB taxonomy
-Example:
    
+
    GTDB taxonomy example:
    
 
    from ete4 import PhyloTree
 
-# load the whole leaf name as species taxid
+# Load the whole leaf name as species taxid.
 newick = '((p__Huberarchaeota,f__Korarchaeaceae)d__Archaea,o__Peptococcales);'
 
-tree= PhyloTree(newick)
+tree = PhyloTree(newick)
 tax2name, tax2track, tax2rank = gtdb.annotate_tree(tree, taxid_attr="name")
 
 print(tree.to_str(props=['sci_name', 'rank']))
-
-"""
-                                        ╭╴p__Huberarchaeota,phylum
-              ╭╴d__Archaea,superkingdom╶┤
-╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
-              │
-              ╰╴o__Peptococcales,order
-"""
+#                                         ╭╴p__Huberarchaeota,phylum
+#               ╭╴d__Archaea,superkingdom╶┤
+# ╴root,no rank╶┤                         ╰╴f__Korarchaeaceae,family
+#               │
+#               ╰╴o__Peptococcales,order
 
    
 
    
 
    
@@ -454,10 +479,16 @@ 
    ETE Toolkit
    
 
 
    Navigation
    
 
    Contents:
    
-
    
diff --git a/tutorial/tutorial_trees.html b/tutorial/tutorial_trees.html
index b45f53884..3a4a4b7aa 100644
--- a/tutorial/tutorial_trees.html
+++ b/tutorial/tutorial_trees.html
@@ -1792,6 +1792,7 @@ 
    Navigation
    
 
  • Working with the Tree structure
    • 
 
  • Phylogenetic trees
    • 
 
  • Programmable tree drawing
    • 
+
  • Taxonomy databases
    • 
 
 
 
  • Reference Guide
    •