diff --git a/_modules/ete4/gtdb_taxonomy/gtdbquery.html b/_modules/ete4/gtdb_taxonomy/gtdbquery.html index 4f6b811e..73881800 100644 --- a/_modules/ete4/gtdb_taxonomy/gtdbquery.html +++ b/_modules/ete4/gtdb_taxonomy/gtdbquery.html @@ -188,18 +188,41 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

#     return taxid, spname, norm_score
 
+    def _get_id2rank(self, internal_taxids):
+        """Given a list of numeric ids (each one representing a taxa in GTDB), return a dictionary with their corresponding ranks.
+        Examples: 
+        > gtdb.get_rank([2174, 205487, 610])
+        {2174: 'family', 205487: 'order', 610: 'phylum'}
+
+        Note: Numeric taxids are not recognized by the official GTDB taxonomy database, only for internal usage.
+        """
+        ids = ','.join('"%s"' % v for v in set(internal_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_rank(self, taxids):
-        """Return dictionary converting taxids to their GTDB taxonomy rank."""
+        """Give a list of GTDB string taxids, return a dictionary with their corresponding ranks.
+        Examples: 
+        
+        > gtdb.get_rank(['c__Thorarchaeia', 'RS_GCF_001477695.1'])
+        {'c__Thorarchaeia': 'class', 'RS_GCF_001477695.1': 'subspecies'}
+        """
+
+        taxid2rank = {}
+        name2ids = self._get_name_translator(taxids)
+        overlap_ids = name2ids.values()
+        taxids = [item for sublist in overlap_ids for item in sublist]
         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()}

+        for tax, rank in result.fetchall():
+            taxid2rank[list(self._get_taxid_translator([tax]).values())[0]] = rank
+        
+        return taxid2rank
-
-[docs] - def get_lineage_translator(self, taxids): + def _get_lineage_translator(self, taxids): """Given a valid taxid number, return its corresponding lineage track as a hierarchically sorted list of parent taxids. """ @@ -211,9 +234,7 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

id2lineages = {}
         for tax, track in result.fetchall():
             id2lineages[tax] = list(map(int, reversed(track.split(","))))
-
-        return id2lineages
- + return id2lineages
[docs] @@ -222,18 +243,16 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

        hierarchically sorted list of parent taxnames.
         """
         name_lineages = []
-        name2taxid = self.get_name_translator(taxnames)
+        name2taxid = self._get_name_translator(taxnames)
         for key, value in name2taxid.items():
-            lineage = self.get_lineage(value[0])
-            names = self.get_taxid_translator(lineage)
+            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): + def _get_lineage(self, taxid): """Given a valid taxid number, return its corresponding lineage track as a hierarchically sorted list of parent taxids. """ @@ -256,8 +275,7 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

warnings.warn("taxid %s was translated into %s" %(taxid, merged_conversion[taxid]))
 
         track = list(map(int, raw_track[0].split(",")))
-        return list(reversed(track))
- + return list(reversed(track))
[docs] @@ -272,9 +290,7 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

return id2name
-
-[docs] - def get_taxid_translator(self, taxids, try_synonyms=True): + def _get_taxid_translator(self, taxids, try_synonyms=True): """Given a list of taxids, returns a dictionary with their corresponding scientific names. """ @@ -302,12 +318,9 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

#         for tax, spname in result.fetchall():
         #             id2name[new2old[tax]] = spname
 
-        return id2name
+ return id2name - -
-[docs] - def get_name_translator(self, names): + 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. @@ -336,21 +349,17 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

oname = name2origname[sp.lower()]
                 name2id.setdefault(oname, []).append(taxid)
                 #name2realname[oname] = sp
-        return name2id
- + return name2id -
-[docs] - def translate_to_names(self, taxids): + 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) + id2name = self._get_taxid_translator(taxids) names = [] for sp in taxids: names.append(id2name.get(sp, sp)) - return names
- + return names
@@ -364,7 +373,7 @@

Source code for ete4.gtdb_taxonomy.gtdbquery

taxid = int(parent)
         except ValueError:
             try:
-                taxid = self.get_name_translator([parent])[parent][0]
+                taxid = self._get_name_translator([parent])[parent][0]
             except KeyError:
                 raise ValueError('%s not found!' %parent)
 
@@ -390,7 +399,7 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
elif found == 1:
             return [taxid]
         if rank_limit or collapse_subspecies or return_tree:
-            descendants_spnames = self.get_taxid_translator(list(descendants.keys()))
+            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:
@@ -401,10 +410,10 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
return [n.name for n in tree]
 
         elif intermediate_nodes:
-            return self.translate_to_names([tid for tid, count in descendants.items()])
+            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])

+            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])

 
 
 

@@ -427,7 +436,7 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
        """
         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]}
+        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:
@@ -447,7 +456,7 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
# 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))
+            tax2name = self._get_taxid_translator(list(subtree))
             name2tax ={spname:taxid for taxid,spname in tax2name.items()}
             nodes[root_taxid] = PhyloTree({'name': str(root_taxid)})
             current_parent = nodes[root_taxid]
@@ -465,15 +474,15 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
taxids = set(map(int, taxids))
             sp2track = {}
             elem2node = {}
-            id2lineage = self.get_lineage_translator(taxids)
+            id2lineage = self._get_lineage_translator(taxids)
             all_taxids = set()
             for lineage in id2lineage.values():
                 all_taxids.update(lineage)
-            id2rank = self.get_rank(all_taxids)
+            id2rank = self._get_id2rank(all_taxids)
 
-            tax2name = self.get_taxid_translator(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())))
+            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()}
 
@@ -523,15 +532,15 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
n.detach()
 
         if annotate:
-            self.annotate_tree(tree)
+            self.annotate_tree(tree, ignore_unclassified=False)
 
         return tree

 
 
 

 [docs]
-    def annotate_tree(self, t, taxid_attr='name',
-                      tax2name=None, tax2track=None, tax2rank=None):
+    def annotate_tree(self, t, taxid_attr='name', tax2name=None, 
+                        tax2track=None, tax2rank=None, ignore_unclassified=False):
         """Annotate a tree containing taxids as leaf names.
 
         It annotates by adding the properties 'taxid', 'sci_name',
@@ -555,7 +564,7 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
try:
                     # translate gtdb name -> id
                     taxaname = getattr(n, taxid_attr, n.props.get(taxid_attr))
-                    tid = self.get_name_translator([taxaname])[taxaname][0]
+                    tid = self._get_name_translator([taxaname])[taxaname][0]
                     taxids.add(tid)
                 except (KeyError, ValueError, AttributeError):
                     pass
@@ -564,18 +573,18 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
taxids, merged_conversion = self._translate_merged(taxids)
 
         if not tax2name or taxids - set(map(int, list(tax2name.keys()))):
-            tax2name = self.get_taxid_translator(taxids)
+            tax2name = self._get_taxid_translator(taxids)
         if not tax2track or taxids - set(map(int, list(tax2track.keys()))):
-            tax2track = self.get_lineage_translator(taxids)
-
+            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())))
+        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()))
+            tax2rank = self._get_id2rank(list(tax2name.keys()))
 
         name2tax ={spname:taxid for taxid,spname in tax2name.items()}
         n2leaves = t.get_cached_content()
@@ -586,10 +595,8 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
else:
                 node_taxid = None
             node.add_prop('taxid', node_taxid)
-
             if node_taxid:
-                tmp_taxid = self.get_name_translator([node_taxid]).get(node_taxid, [None])[0]
-
+                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]
 
@@ -613,16 +620,30 @@ 
Source code for ete4.gtdb_taxonomy.gtdbquery
rank = 'Unknown',
                                named_lineage = [])
             else:
-                lineage = self._common_lineage([lf.props.get('lineage') for lf in n2leaves[node]])
+                
+                if ignore_unclassified:
+                    vectors = [lf.props.get('lineage') for lf in n2leaves[node] if lf.props.get('lineage')]
+                else:
+                    vectors = [lf.props.get('lineage') for lf in n2leaves[node]]
+                lineage = self._common_lineage(vectors)
+                
+                rank = tax2rank.get(lineage[-1], 'Unknown')
+                
                 if lineage[-1]:
-                    ancestor = self.get_taxid_translator([lineage[-1]])[lineage[-1]]
+                    if rank != 'subspecies':
+                        ancestor = self._get_taxid_translator([lineage[-1]])[lineage[-1]]
+                    else:
+                        ancestor = self._get_taxid_translator([lineage[-2]])[lineage[-2]]
+                        lineage = lineage[:-1] # remove subspecies from lineage
+                        rank = tax2rank.get(lineage[-1], 'Unknown') # update rank
                 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'),
+                               rank = rank,
                                named_lineage = [tax2name.get(tax, str(tax)) for tax in lineage])
 
         return tax2name, tax2track, tax2rank

diff --git a/_modules/ete4/ncbi_taxonomy/ncbiquery.html b/_modules/ete4/ncbi_taxonomy/ncbiquery.html
index 4278e713..079e3417 100644
--- a/_modules/ete4/ncbi_taxonomy/ncbiquery.html
+++ b/_modules/ete4/ncbi_taxonomy/ncbiquery.html
@@ -532,7 +532,7 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
 [docs]
     def annotate_tree(self, t, taxid_attr="name", tax2name=None,
-                      tax2track=None, tax2rank=None):
+                      tax2track=None, tax2rank=None, ignore_unclassified=False):
         """Annotate a tree containing taxids as leaf names.
 
         The annotation adds the properties: 'taxid', 'sci_name',
@@ -595,14 +595,18 @@ 
Source code for ete4.ncbi_taxonomy.ncbiquery
rank = 'Unknown',
                                named_lineage = [])
             else:
-                lineage = self._common_lineage([lf.props.get('lineage') for lf in n2leaves[n]])
+                if ignore_unclassified:
+                    vectors = [lf.props.get('lineage') for lf in n2leaves[n] if lf.props.get('lineage')]
+                else:
+                    vectors = [lf.props.get('lineage') for lf in n2leaves[n]]
+                lineage = self._common_lineage(vectors)
                 ancestor = lineage[-1]
                 n.add_props(sci_name = tax2name.get(ancestor, str(ancestor)),
-                               common_name = tax2common_name.get(ancestor, ''),
-                               taxid = ancestor,
-                               lineage = lineage,
-                               rank = tax2rank.get(ancestor, 'Unknown'),
-                               named_lineage = [tax2name.get(tax, str(tax)) for tax in lineage])
+                            common_name = tax2common_name.get(ancestor, ''),
+                            taxid = ancestor,
+                            lineage = lineage,
+                            rank = tax2rank.get(ancestor, 'Unknown'),
+                            named_lineage = [tax2name.get(tax, str(tax)) for tax in lineage])
 
         return tax2name, tax2track, tax2rank

 
diff --git a/_modules/ete4/phylo/phylotree.html b/_modules/ete4/phylo/phylotree.html
index dbf6636b..9800194d 100644
--- a/_modules/ete4/phylo/phylotree.html
+++ b/_modules/ete4/phylo/phylotree.html
@@ -728,7 +728,7 @@ 
Source code for ete4.phylo.phylotree
 
 

 [docs]
-    def annotate_ncbi_taxa(self, taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None):
+    def annotate_ncbi_taxa(self, taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None, ignore_unclassified=False):
         """Add NCBI taxonomy annotation to all descendant nodes. Leaf nodes are
         expected to contain a feature (name, by default) encoding a valid taxid
         number.
@@ -780,14 +780,14 @@ 
Source code for ete4.phylo.phylotree
         """
 
         ncbi = NCBITaxa(dbfile=dbfile)
-        return ncbi.annotate_tree(self, taxid_attr=taxid_attr, tax2name=tax2name, tax2track=tax2track, tax2rank=tax2rank)

+        return ncbi.annotate_tree(self, taxid_attr=taxid_attr, tax2name=tax2name, tax2track=tax2track, tax2rank=tax2rank, ignore_unclassified=ignore_unclassified)

 
 
 

 [docs]
-    def annotate_gtdb_taxa(self, taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None):
+    def annotate_gtdb_taxa(self, taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None, ignore_unclassified=False):
         gtdb = GTDBTaxa(dbfile=dbfile)
-        return gtdb.annotate_tree(self, taxid_attr=taxid_attr, tax2name=tax2name, tax2track=tax2track, tax2rank=tax2rank)

+        return gtdb.annotate_tree(self, taxid_attr=taxid_attr, tax2name=tax2name, tax2track=tax2track, tax2rank=tax2rank, ignore_unclassified=ignore_unclassified)

 
 
 

diff --git a/genindex.html b/genindex.html
index b30aa0e3..ec024143 100644
--- a/genindex.html
+++ b/genindex.html
@@ -926,20 +926,12 @@ 
G

 
       
  • get_line_type() (in module ete4.smartview.renderer.draw_helpers)
 
    • 
-      
  • get_lineage() (GTDBTaxa method)
-
-      
    • 
   
   
       
  • touch_and_get() (in module ete4.smartview.gui.server)
 
    • 
-      
  • translate_to_names() (GTDBTaxa method)
-
-      
    • 
       
  • traverse() (in module ete4.core.operations)
 
       
      
diff --git a/objects.inv b/objects.inv
index 58e0e3c8..bdaff0e4 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/reference/reference_phylo.html b/reference/reference_phylo.html
index f2811416..46683dfa 100644
--- a/reference/reference_phylo.html
+++ b/reference/reference_phylo.html
@@ -69,12 +69,12 @@ 
      PhyloTree
 
      
-annotate_gtdb_taxa(taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None)[source]
      
+annotate_gtdb_taxa(taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None, ignore_unclassified=False)[source]
 
      
 
 
      
 
      
-annotate_ncbi_taxa(taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None)[source]
      
+annotate_ncbi_taxa(taxid_attr='species', tax2name=None, tax2track=None, tax2rank=None, dbfile=None, ignore_unclassified=False)[source]
 
      Add NCBI taxonomy annotation to all descendant nodes. Leaf nodes are
 expected to contain a feature (name, by default) encoding a valid taxid
 number.
      
diff --git a/reference/reference_smartview.html b/reference/reference_smartview.html
index 38b5708d..1e2fedbc 100644
--- a/reference/reference_smartview.html
+++ b/reference/reference_smartview.html
@@ -92,7 +92,7 @@ 
      Smartview (web graphi
 
 
      
 
      
-class TreeData(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7fa23ab236a0> = None, searches: dict = None)[source]
      
+class TreeData(tree: ete4.core.tree.Tree = None, name: str = None, style: ete4.smartview.renderer.treestyle.TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: <function namedtuple at 0x7f7bf87276a0> = None, searches: dict = None)[source]
 
      
 
      
 __init__(tree: Tree = None, name: str = None, style: TreeStyle = None, nodestyles: dict = None, include_props: list = None, exclude_props: list = None, layouts: list = None, timer: float = None, ultrametric: bool = False, initialized: bool = False, selected: dict = None, active: namedtuple = None, searches: dict = None) → None
      
diff --git a/reference/reference_taxonomy.html b/reference/reference_taxonomy.html
index f73a156e..6c183d8e 100644
--- a/reference/reference_taxonomy.html
+++ b/reference/reference_taxonomy.html
@@ -53,7 +53,7 @@ 
      NCBITaxa
 
 
      
 
      
-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, ignore_unclassified=False)[source]
 
      Annotate a tree containing taxids as leaf names.
      
 
      The annotation adds the properties: ‘taxid’, ‘sci_name’,
 ‘lineage’, ‘named_lineage’ and ‘rank’.
      
@@ -201,7 +201,7 @@ 
      GTDBTaxa
 
 
      
 
      
-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, ignore_unclassified=False)[source]
 
      Annotate a tree containing taxids as leaf names.
      
 
      It annotates by adding the properties ‘taxid’, ‘sci_name’,
 ‘lineage’, ‘named_lineage’ and ‘rank’.
      
@@ -240,20 +240,6 @@ 
      GTDBTaxa
 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]
      
@@ -261,24 +247,13 @@ 
      GTDBTaxa
 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.
      
+
      Give a list of GTDB string taxids, return a dictionary with their corresponding ranks.
+Examples:
      
+
      > gtdb.get_rank([‘c__Thorarchaeia’, ‘RS_GCF_001477695.1’])
+{‘c__Thorarchaeia’: ‘class’, ‘RS_GCF_001477695.1’: ‘subspecies’}
      
 
      
 
 
      
@@ -304,12 +279,6 @@ 
      GTDBTaxa
 
      
 
      
 
-
      
-
      
-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]
      
diff --git a/searchindex.js b/searchindex.js
index db364e13..6720dd97 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1) Layout Tab": [[16, "layout-tab"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "3) Advanced Tab": [[16, "advanced-tab"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "About": [[0, "about"]], "Add legend": [[16, "add-legend"]], "Add legend and title": [[20, "add-legend-and-title"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Advanced traversing": [[19, "advanced-traversing"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "Bar Plot": [[16, "bar-plot"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "Can I control the order in which nodes are visited?": [[1, "can-i-control-the-order-in-which-nodes-are-visited"]], "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"]], "Change branch length scale (zoom in x)": [[20, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[20, "change-branch-separation-between-nodes-zoom-in-y"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Color Strip": [[16, "color-strip"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Comparing trees": [[19, "comparing-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "contents"]], "Contents:": [[2, null]], "Control Panel": [[16, "control-panel"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Distances between trees": [[19, "distances-between-trees"]], "Domain annotation": [[16, "domain-annotation"]], "Download": [[16, "download"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "EvolEvent": [[7, "evolevent"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Expression search": [[16, "expression-search"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "General": [[1, "general"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Getting taxid information": [[17, "getting-taxid-information"]], "Heatmap": [[16, "heatmap"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "How do I find a leaf by its name?": [[1, "how-do-i-find-a-leaf-by-its-name"]], "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 use ETE?": [[1, "how-do-i-use-ete"]], "How do I visit all nodes within a tree?": [[1, "how-do-i-visit-all-nodes-within-a-tree"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Img faces": [[20, "img-faces"]], "Implementation": [[15, "implementation"]], "Indices and tables": [[2, "indices-and-tables"]], "Interactive sessions": [[16, "interactive-sessions"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Layout functions": [[20, "layout-functions"]], "Layouts": [[9, "layouts"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "NCBITaxa": [[10, "ncbitaxa"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Node Panel": [[16, "node-panel"]], "Node annotation": [[19, "node-annotation"]], "Node backgrounds": [[20, "node-backgrounds"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Node style": [[16, "node-style"], [20, "node-style"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Outside variables": [[18, "outside-variables"]], "Overrall": [[16, "overrall"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "Parsers": [[6, "parsers"]], "PhyloTree": [[7, "phylotree"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Pruning trees": [[19, "pruning-trees"]], "Reading and writing": [[1, "reading-and-writing"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Reference Guide": [[3, "reference-guide"]], "Regular expression search": [[16, "regular-expression-search"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Renderer": [[9, "renderer"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Rotate a tree": [[20, "rotate-a-tree"]], "Search all nodes matching a given criteria": [[19, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria": [[19, "search-nodes-matching-a-given-criteria"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Shortcuts": [[19, "shortcuts"]], "Show leaf node names, branch length and branch support": [[16, "show-leaf-node-names-branch-length-and-branch-support"], [20, "show-leaf-node-names-branch-length-and-branch-support"]], "Showing node\u2019s properties in pop up": [[16, "showing-node-s-properties-in-pop-up"]], "Simple search": [[16, "simple-search"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Standalone scripts": [[16, "standalone-scripts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Topological search": [[16, "topological-search"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree Browsing": [[1, "tree-browsing"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "Tree rooting": [[19, "tree-rooting"]], "Tree style": [[20, "tree-style"]], "Tree visualization": [[1, "tree-visualization"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Trees": [[19, "trees"]], "Trees within trees": [[20, "trees-within-trees"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Verbose mode": [[16, "verbose-mode"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Writing newick trees": [[19, "writing-newick-trees"]], "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"]]}, "docnames": ["about", "faqs", "index", "reference/index", "reference/reference_clustering", "reference/reference_operations", "reference/reference_parsers", "reference/reference_phylo", "reference/reference_seqgroup", "reference/reference_smartview", "reference/reference_taxonomy", "reference/reference_tree", "reference/reference_treematcher", "reference/reference_treeview", "tutorial/index", "tutorial/tutorial_phylogeny", "tutorial/tutorial_smartview", "tutorial/tutorial_taxonomy", "tutorial/tutorial_treematcher", "tutorial/tutorial_trees", "tutorial/tutorial_treeview"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["about.rst", "faqs.rst", "index.rst", "reference/index.rst", "reference/reference_clustering.rst", "reference/reference_operations.rst", "reference/reference_parsers.rst", "reference/reference_phylo.rst", "reference/reference_seqgroup.rst", "reference/reference_smartview.rst", "reference/reference_taxonomy.rst", "reference/reference_tree.rst", "reference/reference_treematcher.rst", "reference/reference_treeview.rst", "tutorial/index.rst", "tutorial/tutorial_phylogeny.rst", "tutorial/tutorial_smartview.rst", "tutorial/tutorial_taxonomy.rst", "tutorial/tutorial_treematcher.rst", "tutorial/tutorial_trees.rst", "tutorial/tutorial_treeview.rst"], "indexentries": {"__init__() (alignedgrid method)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid.__init__", false]], "__init__() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.__init__", false]], "__init__() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.__init__", false]], "__init__() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.__init__", false]], "__init__() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.__init__", false]], "__init__() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.__init__", false]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__", false]], "__init__() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.__init__", false]], "__init__() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.__init__", false]], "__init__() (face method)": [[9, "ete4.smartview.renderer.faces.Face.__init__", false]], "__init__() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.__init__", false]], "__init__() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.__init__", false]], "__init__() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.__init__", false]], "__init__() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.__init__", false]], "__init__() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.__init__", false]], "__init__() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.__init__", false]], "__init__() (layoutbestname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName.__init__", false]], "__init__() (layoutbigg method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg.__init__", false]], "__init__() (layoutbranchlength method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength.__init__", false]], "__init__() (layoutbranchsupport method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport.__init__", false]], "__init__() (layoutcard method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard.__init__", false]], "__init__() (layoutcazy method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy.__init__", false]], "__init__() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.__init__", false]], "__init__() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.__init__", false]], "__init__() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.__init__", false]], "__init__() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.__init__", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.__init__", false]], "__init__() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.__init__", false]], "__init__() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.__init__", false]], "__init__() (layoutkeggenzyme method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme.__init__", false]], "__init__() (layoutkeggmodule method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule.__init__", false]], "__init__() (layoutkeggnumber method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber.__init__", false]], "__init__() (layoutkeggpathway method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway.__init__", false]], "__init__() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.__init__", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.__init__", false]], "__init__() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.__init__", false]], "__init__() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.__init__", false]], "__init__() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.__init__", false]], "__init__() (layoutpdb method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb.__init__", false]], "__init__() (layoutpfamdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains.__init__", false], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains.__init__", false]], "__init__() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.__init__", false]], "__init__() (layoutproteinname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName.__init__", false]], "__init__() (layoutscientificname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName.__init__", false]], "__init__() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.__init__", false]], "__init__() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.__init__", false]], "__init__() (layoutsmartdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains.__init__", false], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains.__init__", false]], "__init__() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.__init__", false]], "__init__() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__", false]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__", false]], "__init__() (ncbitaxa method)": [[10, "ete4.NCBITaxa.__init__", false]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__", false]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__", false]], "__init__() (phylotree method)": [[7, "ete4.PhyloTree.__init__", false]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__", false]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__", false]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__", false]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__", false]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__", false]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__", false]], "__init__() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.__init__", false]], "__init__() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.__init__", false]], "__init__() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.__init__", false]], "__init__() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.__init__", false]], "__init__() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.__init__", false]], "__init__() (tree method)": [[11, "ete4.Tree.__init__", false]], "__init__() (treedata method)": [[9, "ete4.smartview.gui.server.TreeData.__init__", false]], "__init__() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.__init__", false]], "__init__() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.__init__", false]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__", false]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade", false]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node", false]], "active (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Active", false]], "active (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.active", false]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face", false]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos", false]], "add_branch_values() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_branch_values", false]], "add_child() (tree method)": [[11, "ete4.Tree.add_child", false]], "add_children() (tree method)": [[11, "ete4.Tree.add_children", false]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face", false]], "add_face() (tree method)": [[11, "ete4.Tree.add_face", false]], "add_face_smartview() (tree method)": [[11, "ete4.Tree.add_face_smartview", false]], "add_face_treeview() (tree method)": [[11, "ete4.Tree.add_face_treeview", false]], "add_feature() (tree method)": [[11, "ete4.Tree.add_feature", false]], "add_features() (tree method)": [[11, "ete4.Tree.add_features", false]], "add_leaf_names() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_leaf_names", false]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend", false]], "add_next_branch() (walker method)": [[5, "ete4.core.operations.Walker.add_next_branch", false]], "add_prop() (tree method)": [[11, "ete4.Tree.add_prop", false]], "add_props() (tree method)": [[11, "ete4.Tree.add_props", false]], "add_sister() (tree method)": [[11, "ete4.Tree.add_sister", false]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree", false]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request", false]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer", false]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header", false]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid", false]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace", false]], "alignmentface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignmentFace", false]], "ancestors() (tree method)": [[11, "ete4.Tree.ancestors", false]], "annotate_gtdb_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_gtdb_taxa", false]], "annotate_ncbi_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_ncbi_taxa", false]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree", false]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree", false]], "apply_translations() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.apply_translations", false]], "arrowface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ArrowFace", false]], "assert_root_consistency() (in module ete4.core.operations)": [[5, "ete4.core.operations.assert_root_consistency", false]], "attrface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AttrFace", false]], "box (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Box", false]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks", false]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions", false]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback", false]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian", false]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name", false]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name", false]], "check_monophyly() (tree method)": [[11, "ete4.Tree.check_monophyly", false]], "children (tree attribute)": [[11, "ete4.Tree.children", false]], "circleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.CircleFace", false]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec", false]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect", false]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades", false]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles", false]], "clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree", false]], "collapse_lineage_specific_expansions() (phylotree method)": [[7, "ete4.PhyloTree.collapse_lineage_specific_expansions", false]], "collapse_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE", false]], "collapsed_faces (tree attribute)": [[11, "ete4.Tree.collapsed_faces", false]], "common_ancestor() (in module ete4.core.operations)": [[5, "ete4.core.operations.common_ancestor", false]], "common_ancestor() (tree method)": [[11, "ete4.Tree.common_ancestor", false]], "compare() (tree method)": [[11, "ete4.Tree.compare", false]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box", false]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box", false]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box", false]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box", false]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box", false]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box", false]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box", false]], "compute_bounding_box() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box", false]], "compute_bounding_box() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box", false]], "compute_bounding_box() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box", false]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize", false]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie", false]], "content_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.content_repr", false]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size", false]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size", false]], "cophenetic_matrix() (tree method)": [[11, "ete4.Tree.cophenetic_matrix", false]], "copy() (tree method)": [[11, "ete4.Tree.copy", false]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style", false]], "create_dichotomic_sister() (in module ete4.core.operations)": [[5, "ete4.core.operations.create_dichotomic_sister", false]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade", false]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node", false]], "del_feature() (tree method)": [[11, "ete4.Tree.del_feature", false]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop", false]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree", false]], "delete() (tree method)": [[11, "ete4.Tree.delete", false]], "descendants() (tree method)": [[11, "ete4.Tree.descendants", false]], "describe() (tree method)": [[11, "ete4.Tree.describe", false]], "detach() (tree method)": [[11, "ete4.Tree.detach", false]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation", false]], "dist (tree attribute)": [[11, "ete4.Tree.dist", false]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist", false]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw", false]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw", false]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw", false]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw", false]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw", false]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw", false]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw", false]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw", false]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw", false]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw", false]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw", false]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw", false]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw", false]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw", false]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw", false]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw", false]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers", false]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc", false]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array", false]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow", false]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline", false]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline", false]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle", false]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed", false]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed", false]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed", false]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed", false]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed", false]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content", false]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse", false]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html", false]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img", false]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline", false]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline", false]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line", false]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node", false]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node", false]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node", false]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox", false]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox", false]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox", false]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot", false]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot", false]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline", false]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect", false]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus", false]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice", false]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text", false]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle", false]], "drawer (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Drawer", false]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces", false]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces", false]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc", false]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces", false]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRect", false]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces", false]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size", false]], "dump() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dump", false]], "dumps() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dumps", false]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx", false]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx", false]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy", false]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy", false]], "edges() (tree method)": [[11, "ete4.Tree.edges", false]], "error() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.error", false]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree", false]], "ete4.core.operations": [[5, "module-ete4.core.operations", false]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup", false]], "ete4.parser.newick": [[6, "module-ete4.parser.newick", false]], "ete4.parser.nexus": [[6, "module-ete4.parser.nexus", false]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server", false]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers", false]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer", false]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions", false]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces", false]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts", false]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts", false]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts", false]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts", false]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts", false]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle", false]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout", false]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle", false]], "ete4.treematcher.treematcher": [[12, "module-ete4.treematcher.treematcher", false]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent", false]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props", false]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies", false]], "explore() (tree method)": [[11, "ete4.Tree.explore", false]], "face (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.Face", false]], "faces (tree attribute)": [[11, "ete4.Tree.faces", false]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest", false]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant", false]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node", false]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value", false]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit", false]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits", false]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits", false]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits", false]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits", false]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits", false]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline", false]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline", false]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table", false]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio", false]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children", false]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade", false]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades", false]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age", false]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup", false]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec", false]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box", false]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box", false]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box", false]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box", false]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box", false]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches", false]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches", false]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content", false]], "get_children() (tree method)": [[11, "ete4.Tree.get_children", false]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf", false]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node", false]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color", false]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search", false]], "get_commands() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_commands", false]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names", false]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names", false]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content", false]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content", false]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context", false]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events", false]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa", false]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa", false]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance", false]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer", false]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers", false]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn", false]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active", false]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries", false]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search", false]], "get_extended_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_extended_props", false]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf", false]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node", false]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf", false]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node", false]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation", false]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype", false]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames", false]], "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", false]], "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", false]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname", false]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts", false]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters", false]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend", false]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type", false]], "get_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage", false]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage", false]], "get_lineage_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_lineage_translator", false]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator", false]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup", false]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic", false]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events", false]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage", false]], "get_name_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_translator", false]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator", false]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick", false]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port", false]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info", false]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline", false]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents", false]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser", false]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props", false]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop", false]], "get_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_props", false]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank", false]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank", false]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect", false]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function", false]], "get_section() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_section", false]], "get_sections() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_sections", false]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children", false]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info", false]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections", false]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq", false]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq", false]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq", false]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette", false]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters", false]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees", false]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species", false]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats", false]], "get_taxid_translator() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_taxid_translator", false]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator", false]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid", false]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip", false]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search", false]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology", false]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology", false]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id", false]], "get_trees() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_trees", false]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file", false]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form", false]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick", false]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs", false]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys", false]], "globalstuff (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.GlobalStuff", false]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back", false]], "grid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.Grid", false]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa", false]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches", false]], "htmlface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.HTMLFace", false]], "id (tree attribute)": [[11, "ete4.Tree.id", false]], "img_style (tree property)": [[11, "ete4.Tree.img_style", false]], "imgface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ImgFace", false]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport", false]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport", false]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport", false]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props", false]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init", false]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete", false]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick", false]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize", false]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style", false]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized", false]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate", false]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references", false]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist", false]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles", false]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box", false]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment", false]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist", false]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed", false]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed", false]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized", false]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf", false]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic", false]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root", false]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small", false]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small", false]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries", false]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder", false]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species", false]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch", false]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error", false]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize", false]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize", false]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment", false]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName", false]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot", false]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName", false]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg", false]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength", false]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport", false]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard", false]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy", false]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName", false]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance", false]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.evol_events_layouts)": [[9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents", false]], "layoutgenomiccontext (class in ete4.smartview.renderer.layouts.context_layouts)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext", false]], "layouthumanogs (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs", false]], "layoutkeggenzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme", false]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule", false]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber", false]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor", false]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName", false]], "layoutnumberleaves (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves", false]], "layoutoutline (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline", false]], "layoutpdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains", false]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName", false]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName", false]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts", false]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName", false]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName", false]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains", false]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC", false]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans", false]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names", false]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles", false]], "leaves() (tree method)": [[11, "ete4.Tree.leaves", false]], "legendface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.LegendFace", false]], "level (tree attribute)": [[11, "ete4.Tree.level", false]], "lineage() (tree method)": [[11, "ete4.Tree.lineage", false]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment", false]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable", false]], "load() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.load", false]], "load() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.load", false]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree", false]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick", false]], "loads() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.loads", false]], "loads() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.loads", false]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance", false]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box", false]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces", false]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name", false]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name", false]], "make_parser() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.make_parser", false]], "match() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.match", false]], "match() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.match", false]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint", false]], "min_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE", false]], "module": [[4, "module-ete4.clustering.clustertree", false], [5, "module-ete4.core.operations", false], [6, "module-ete4.parser.newick", false], [6, "module-ete4.parser.nexus", false], [8, "module-ete4.core.seqgroup", false], [9, "module-ete4.smartview.gui.server", false], [9, "module-ete4.smartview.renderer.draw_helpers", false], [9, "module-ete4.smartview.renderer.drawer", false], [9, "module-ete4.smartview.renderer.face_positions", false], [9, "module-ete4.smartview.renderer.faces", false], [9, "module-ete4.smartview.renderer.layouts.context_layouts", false], [9, "module-ete4.smartview.renderer.layouts.default_layouts", false], [9, "module-ete4.smartview.renderer.layouts.domain_layouts", false], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false], [9, "module-ete4.smartview.renderer.layouts.seq_layouts", false], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false], [9, "module-ete4.smartview.renderer.layouts.staple_layouts", false], [9, "module-ete4.smartview.renderer.nodestyle", false], [9, "module-ete4.smartview.renderer.treelayout", false], [9, "module-ete4.smartview.renderer.treestyle", false], [12, "module-ete4.treematcher.treematcher", false], [13, "module-treeview", false]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move", false]], "name (tree attribute)": [[11, "ete4.Tree.name", false]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name", false]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare", false]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa", false]], "newickerror": [[6, "ete4.parser.newick.NewickError", false]], "nexuserror": [[6, "ete4.parser.nexus.NexusError", false]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html", false]], "node (walker property)": [[5, "ete4.core.operations.Walker.node", false]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id", false]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size", false]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size", false]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes", false]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle", false]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles", false]], "npanels (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.NPANELS", false]], "npanels (draweraligncircfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS", false]], "npanels (draweralignrectfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS", false]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit", false]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit", false]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window", false]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation", false]], "outlineface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.OutlineFace", false]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Padding", false]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents", false]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree", false]], "piechartface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.PieChartFace", false]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child", false]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate", false]], "populate() (tree method)": [[11, "ete4.Tree.populate", false]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform", false]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule", false]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile", false]], "prop_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.prop_repr", false]], "props (tree attribute)": [[11, "ete4.Tree.props", false]], "prune() (tree method)": [[11, "ete4.Tree.prune", false]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection", false]], "quote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.quote", false]], "read_content() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_content", false]], "read_nodes() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_nodes", false]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile", false]], "rectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.RectFace", false]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang", false]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove", false]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active", false]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade", false]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child", false]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children", false]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search", false]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection", false]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister", false]], "render() (tree method)": [[11, "ete4.Tree.render", false]], "repr_short() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.repr_short", false]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json", false]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy", false]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy", false]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results", false]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts", false]], "retrieve_tree_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data", false]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children", false]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds", false]], "root (tree attribute)": [[11, "ete4.Tree.root", false]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at", false]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview", false]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string", false]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval", false]], "safer_eval() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.safer_eval", false]], "scaleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ScaleFace", false]], "search() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.search", false]], "search() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.search", false]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors", false]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants", false]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name", false]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes", false]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection", false]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches", false]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected", false]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face", false]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos", false]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace", false]], "selectedface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedFace", false]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace", false]], "seqface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqFace", false]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup", false]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace", false]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function", false]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup", false]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style", false]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style", false]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style", false]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style", false]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style", false]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style", false]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style", false]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style", false]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style", false]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style", false]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style", false]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style", false]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style", false]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style", false]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style", false]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style", false]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style", false]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style", false]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style", false]], "set_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_outgroup", false]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup", false]], "set_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.set_seq", false]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function", false]], "set_style() (tree method)": [[11, "ete4.Tree.set_style", false]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style", false]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style", false]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style", false]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style", false]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style", false]], "show() (tree method)": [[11, "ete4.Tree.show", false]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette", false]], "size (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Size", false]], "size (tree attribute)": [[11, "ete4.Tree.size", false]], "skip_quoted_name() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_quoted_name", false]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_spaces_and_comments", false]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style", false]], "sort() (in module ete4.core.operations)": [[5, "ete4.core.operations.sort", false]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort", false]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants", false]], "species (phylotree property)": [[7, "ete4.PhyloTree.species", false]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups", false]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis", false]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack", false]], "stackedbarface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.StackedBarFace", false]], "standardize() (tree method)": [[11, "ete4.Tree.standardize", false]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active", false]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search", false]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection", false]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style", false]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary", false]], "support (tree attribute)": [[11, "ete4.Tree.support", false]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children", false]], "swap_props() (in module ete4.core.operations)": [[5, "ete4.core.operations.swap_props", false]], "textface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.TextFace", false]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer", false]], "to_dendrogram() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_dendrogram", false]], "to_str() (tree method)": [[11, "ete4.Tree.to_str", false]], "to_ultrametric() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_ultrametric", false]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric", false]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get", false]], "translate_to_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.translate_to_names", false]], "translate_to_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.translate_to_names", false]], "traverse() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse", false]], "traverse() (tree method)": [[11, "ete4.Tree.traverse", false]], "traverse_bfs() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse_bfs", false]], "tree (class in ete4)": [[11, "ete4.Tree", false]], "tree (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.tree", false]], "treeactive (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.TreeActive", false]], "treedata (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.TreeData", false]], "treelayout (class in ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout", false]], "treepattern (class in ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.TreePattern", false]], "treestyle (class in ete4.smartview.renderer.treestyle)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle", false]], "treeview": [[13, "module-treeview", false]], "type (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.TYPE", false]], "type (drawercirc attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.TYPE", false]], "type (drawerrect attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.TYPE", false]], "ultrametric (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.ultrametric", false]], "unquote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.unquote", false]], "unroot() (in module ete4.core.operations)": [[5, "ete4.core.operations.unroot", false]], "unroot() (tree method)": [[11, "ete4.Tree.unroot", false]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node", false]], "up (tree attribute)": [[11, "ete4.Tree.up", false]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts", false]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts", false]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props", false]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style", false]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection", false]], "update_size() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_size", false]], "update_sizes_all() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_all", false]], "update_sizes_from() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_from", false]], "update_taxonomy_database() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.update_taxonomy_database", false]], "update_taxonomy_database() (ncbitaxa method)": [[10, "ete4.NCBITaxa.update_taxonomy_database", false]], "walk() (in module ete4.core.operations)": [[5, "ete4.core.operations.walk", false]], "walker (class in ete4.core.operations)": [[5, "ete4.core.operations.Walker", false]], "write() (phylotree method)": [[7, "ete4.PhyloTree.write", false]], "write() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.write", false]], "write() (tree method)": [[11, "ete4.Tree.write", false]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x", false]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x", false]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y", false]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y", false]]}, "objects": {"": [[13, 4, 0, "-", "treeview"]], "ete4": [[10, 0, 1, "", "GTDBTaxa"], [10, 0, 1, "", "NCBITaxa"], [7, 0, 1, "", "PhyloTree"], [11, 0, 1, "", "Tree"]], "ete4.GTDBTaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_lineage"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.NCBITaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_fuzzy_name_translation"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.PhyloTree": [[7, 1, 1, "", "__init__"], [7, 1, 1, "", "annotate_gtdb_taxa"], [7, 1, 1, "", "annotate_ncbi_taxa"], [7, 1, 1, "", "collapse_lineage_specific_expansions"], [7, 1, 1, "", "get_age"], [7, 1, 1, "", "get_age_balanced_outgroup"], [7, 1, 1, "", "get_descendant_evol_events"], [7, 1, 1, "", "get_farthest_oldest_leaf"], [7, 1, 1, "", "get_farthest_oldest_node"], [7, 1, 1, "", "get_my_evol_events"], [7, 1, 1, "", "get_speciation_trees"], [7, 1, 1, "", "get_species"], [7, 1, 1, "", "iter_species"], [7, 1, 1, "", "link_to_alignment"], [7, 1, 1, "", "ncbi_compare"], [7, 1, 1, "", "reconcile"], [7, 1, 1, "", "set_species_naming_function"], [7, 2, 1, "", "species"], [7, 1, 1, "", "split_by_dups"], [7, 1, 1, "", "write"]], "ete4.Tree": [[11, 1, 1, "", "__init__"], [11, 1, 1, "", "add_child"], [11, 1, 1, "", "add_children"], [11, 1, 1, "", "add_face"], [11, 1, 1, "", "add_face_smartview"], [11, 1, 1, "", "add_face_treeview"], [11, 1, 1, "", "add_feature"], [11, 1, 1, "", "add_features"], [11, 1, 1, "", "add_prop"], [11, 1, 1, "", "add_props"], [11, 1, 1, "", "add_sister"], [11, 1, 1, "", "ancestors"], [11, 1, 1, "", "check_monophyly"], [11, 3, 1, "", "children"], [11, 3, 1, "", "collapsed_faces"], [11, 1, 1, "", "common_ancestor"], [11, 1, 1, "", "compare"], [11, 1, 1, "", "cophenetic_matrix"], [11, 1, 1, "", "copy"], [11, 1, 1, "", "del_feature"], [11, 1, 1, "", "del_prop"], [11, 1, 1, "", "delete"], [11, 1, 1, "", "descendants"], [11, 1, 1, "", "describe"], [11, 1, 1, "", "detach"], [11, 3, 1, "", "dist"], [11, 1, 1, "", "edges"], [11, 1, 1, "", "expand_polytomies"], [11, 1, 1, "", "explore"], [11, 3, 1, "", "faces"], [11, 1, 1, "", "from_parent_child_table"], [11, 1, 1, "", "from_skbio"], [11, 1, 1, "", "get_cached_content"], [11, 1, 1, "", "get_children"], [11, 1, 1, "", "get_closest_leaf"], [11, 1, 1, "", "get_distance"], [11, 1, 1, "", "get_farthest_leaf"], [11, 1, 1, "", "get_farthest_node"], [11, 1, 1, "", "get_midpoint_outgroup"], [11, 1, 1, "", "get_monophyletic"], [11, 1, 1, "", "get_prop"], [11, 1, 1, "", "get_sisters"], [11, 1, 1, "", "get_topology_id"], [11, 3, 1, "", "id"], [11, 2, 1, "", "img_style"], [11, 1, 1, "", "init_from_ete"], [11, 1, 1, "", "init_from_newick"], [11, 2, 1, "", "is_collapsed"], [11, 2, 1, "", "is_initialized"], [11, 3, 1, "", "is_leaf"], [11, 1, 1, "", "is_monophyletic"], [11, 3, 1, "", "is_root"], [11, 1, 1, "", "iter_prepostorder"], [11, 1, 1, "", "ladderize"], [11, 1, 1, "", "leaf_names"], [11, 1, 1, "", "leaves"], [11, 3, 1, "", "level"], [11, 1, 1, "", "lineage"], [11, 3, 1, "", "name"], [11, 1, 1, "", "pop_child"], [11, 1, 1, "", "populate"], [11, 3, 1, "", "props"], [11, 1, 1, "", "prune"], [11, 1, 1, "", "remove_child"], [11, 1, 1, "", "remove_children"], [11, 1, 1, "", "remove_sister"], [11, 1, 1, "", "render"], [11, 1, 1, "", "resolve_polytomy"], [11, 1, 1, "", "reverse_children"], [11, 1, 1, "", "robinson_foulds"], [11, 3, 1, "", "root"], [11, 1, 1, "", "search_ancestors"], [11, 1, 1, "", "search_descendants"], [11, 1, 1, "", "search_leaves_by_name"], [11, 1, 1, "", "search_nodes"], [11, 1, 1, "", "set_outgroup"], [11, 1, 1, "", "set_style"], [11, 1, 1, "", "show"], [11, 3, 1, "", "size"], [11, 2, 1, "", "sm_style"], [11, 1, 1, "", "sort_descendants"], [11, 1, 1, "", "standardize"], [11, 3, 1, "", "support"], [11, 1, 1, "", "swap_children"], [11, 1, 1, "", "to_str"], [11, 1, 1, "", "to_ultrametric"], [11, 1, 1, "", "traverse"], [11, 1, 1, "", "unroot"], [11, 3, 1, "", "up"], [11, 1, 1, "", "write"]], "ete4.clustering": [[4, 4, 0, "-", "clustertree"]], "ete4.clustering.clustertree": [[4, 0, 1, "", "ClusterTree"]], "ete4.clustering.clustertree.ClusterTree": [[4, 1, 1, "", "__init__"], [4, 2, 1, "", "deviation"], [4, 1, 1, "", "get_dunn"], [4, 1, 1, "", "get_silhouette"], [4, 2, 1, "", "intercluster_dist"], [4, 2, 1, "", "intracluster_dist"], [4, 1, 1, "", "leaf_profiles"], [4, 1, 1, "", "link_to_arraytable"], [4, 2, 1, "", "profile"], [4, 1, 1, "", "set_distance_function"], [4, 2, 1, "", "silhouette"]], "ete4.core": [[5, 4, 0, "-", "operations"], [8, 4, 0, "-", "seqgroup"]], "ete4.core.operations": [[5, 0, 1, "", "Walker"], [5, 5, 1, "", "add_branch_values"], [5, 5, 1, "", "add_leaf_names"], [5, 5, 1, "", "assert_root_consistency"], [5, 5, 1, "", "common_ancestor"], [5, 5, 1, "", "create_dichotomic_sister"], [5, 5, 1, "", "farthest"], [5, 5, 1, "", "farthest_descendant"], [5, 5, 1, "", "insert_intermediate"], [5, 5, 1, "", "interchange_references"], [5, 5, 1, "", "join_branch"], [5, 5, 1, "", "ladderize"], [5, 5, 1, "", "make_name"], [5, 5, 1, "", "midpoint"], [5, 5, 1, "", "move"], [5, 5, 1, "", "populate"], [5, 5, 1, "", "populate_uniform"], [5, 5, 1, "", "populate_yule"], [5, 5, 1, "", "rehang"], [5, 5, 1, "", "remove"], [5, 5, 1, "", "resolve_polytomy"], [5, 5, 1, "", "root_at"], [5, 5, 1, "", "set_midpoint_outgroup"], [5, 5, 1, "", "set_outgroup"], [5, 5, 1, "", "sort"], [5, 5, 1, "", "swap_props"], [5, 5, 1, "", "to_dendrogram"], [5, 5, 1, "", "to_ultrametric"], [5, 5, 1, "", "traverse"], [5, 5, 1, "", "traverse_bfs"], [5, 5, 1, "", "unroot"], [5, 5, 1, "", "update_size"], [5, 5, 1, "", "update_sizes_all"], [5, 5, 1, "", "update_sizes_from"], [5, 5, 1, "", "walk"]], "ete4.core.operations.Walker": [[5, 1, 1, "", "add_next_branch"], [5, 2, 1, "", "first_visit"], [5, 1, 1, "", "go_back"], [5, 2, 1, "", "has_unvisited_branches"], [5, 2, 1, "", "node"], [5, 2, 1, "", "node_id"]], "ete4.core.seqgroup": [[8, 0, 1, "", "SeqGroup"]], "ete4.core.seqgroup.SeqGroup": [[8, 1, 1, "", "__init__"], [8, 1, 1, "", "get_entries"], [8, 1, 1, "", "get_seq"], [8, 1, 1, "", "iter_entries"], [8, 1, 1, "", "set_seq"], [8, 1, 1, "", "write"]], "ete4.parser": [[6, 4, 0, "-", "newick"], [6, 4, 0, "-", "nexus"]], "ete4.parser.newick": [[6, 6, 1, "", "NewickError"], [6, 5, 1, "", "content_repr"], [6, 5, 1, "", "dump"], [6, 5, 1, "", "dumps"], [6, 5, 1, "", "error"], [6, 5, 1, "", "get_extended_props"], [6, 5, 1, "", "get_props"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"], [6, 5, 1, "", "make_parser"], [6, 5, 1, "", "prop_repr"], [6, 5, 1, "", "quote"], [6, 5, 1, "", "read_content"], [6, 5, 1, "", "read_nodes"], [6, 5, 1, "", "repr_short"], [6, 5, 1, "", "skip_quoted_name"], [6, 5, 1, "", "skip_spaces_and_comments"], [6, 5, 1, "", "unquote"]], "ete4.parser.nexus": [[6, 6, 1, "", "NexusError"], [6, 5, 1, "", "apply_translations"], [6, 5, 1, "", "get_commands"], [6, 5, 1, "", "get_section"], [6, 5, 1, "", "get_sections"], [6, 5, 1, "", "get_trees"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"]], "ete4.phylo": [[7, 0, 1, "", "EvolEvent"]], "ete4.smartview.gui": [[9, 4, 0, "-", "server"]], "ete4.smartview.gui.server": [[9, 0, 1, "", "GlobalStuff"], [9, 0, 1, "", "TreeData"], [9, 5, 1, "", "activate_clade"], [9, 5, 1, "", "activate_node"], [9, 5, 1, "", "add_tree"], [9, 5, 1, "", "add_trees_from_request"], [9, 5, 1, "", "callback"], [9, 5, 1, "", "change_selection_name"], [9, 5, 1, "", "copy_style"], [9, 5, 1, "", "deactivate_clade"], [9, 5, 1, "", "deactivate_node"], [9, 5, 1, "", "del_tree"], [9, 5, 1, "", "find_node"], [9, 5, 1, "", "get_active_clade"], [9, 5, 1, "", "get_active_clades"], [9, 5, 1, "", "get_command_search"], [9, 5, 1, "", "get_drawer"], [9, 5, 1, "", "get_eval_search"], [9, 5, 1, "", "get_layouts"], [9, 5, 1, "", "get_layouts_from_getters"], [9, 5, 1, "", "get_newick"], [9, 5, 1, "", "get_next_available_port"], [9, 5, 1, "", "get_nodes_info"], [9, 5, 1, "", "get_parents"], [9, 5, 1, "", "get_parser"], [9, 5, 1, "", "get_search_function"], [9, 5, 1, "", "get_selection_info"], [9, 5, 1, "", "get_selections"], [9, 5, 1, "", "get_stats"], [9, 5, 1, "", "get_tid"], [9, 5, 1, "", "get_topological_search"], [9, 5, 1, "", "get_trees_from_file"], [9, 5, 1, "", "get_trees_from_form"], [9, 5, 1, "", "get_trees_from_nexus_or_newick"], [9, 5, 1, "", "initialize"], [9, 5, 1, "", "initialize_tree_style"], [9, 5, 1, "", "json_error"], [9, 5, 1, "", "load_tree"], [9, 5, 1, "", "load_tree_from_newick"], [9, 5, 1, "", "maintenance"], [9, 5, 1, "", "make_name"], [9, 5, 1, "", "nice_html"], [9, 5, 1, "", "open_browser_window"], [9, 5, 1, "", "prune_by_selection"], [9, 5, 1, "", "remove_active"], [9, 5, 1, "", "remove_active_clade"], [9, 5, 1, "", "remove_search"], [9, 5, 1, "", "remove_selection"], [9, 5, 1, "", "req_json"], [9, 5, 1, "", "retrieve_layouts"], [9, 5, 1, "", "retrieve_tree_data"], [9, 5, 1, "", "run_smartview"], [9, 5, 1, "", "safer_eval"], [9, 5, 1, "", "search_to_selection"], [9, 5, 1, "", "sort"], [9, 5, 1, "", "store_active"], [9, 5, 1, "", "store_search"], [9, 5, 1, "", "store_selection"], [9, 5, 1, "", "touch_and_get"], [9, 5, 1, "", "unselect_node"], [9, 5, 1, "", "update_app_available_layouts"], [9, 5, 1, "", "update_layouts"], [9, 5, 1, "", "update_node_props"], [9, 5, 1, "", "update_node_style"], [9, 5, 1, "", "update_selection"]], "ete4.smartview.gui.server.TreeData": [[9, 1, 1, "", "__init__"], [9, 3, 1, "", "active"], [9, 3, 1, "", "exclude_props"], [9, 3, 1, "", "include_props"], [9, 3, 1, "", "initialized"], [9, 3, 1, "", "layouts"], [9, 3, 1, "", "name"], [9, 3, 1, "", "nodestyles"], [9, 3, 1, "", "searches"], [9, 3, 1, "", "selected"], [9, 3, 1, "", "style"], [9, 3, 1, "", "timer"], [9, 3, 1, "", "tree"], [9, 3, 1, "", "ultrametric"]], "ete4.smartview.renderer": [[9, 4, 0, "-", "draw_helpers"], [9, 4, 0, "-", "drawer"], [9, 4, 0, "-", "face_positions"], [9, 4, 0, "-", "faces"], [9, 4, 0, "-", "nodestyle"], [9, 4, 0, "-", "treelayout"], [9, 4, 0, "-", "treestyle"]], "ete4.smartview.renderer.draw_helpers": [[9, 0, 1, "", "Box"], [9, 0, 1, "", "Padding"], [9, 5, 1, "", "cartesian"], [9, 5, 1, "", "circumasec"], [9, 5, 1, "", "circumrect"], [9, 5, 1, "", "clip_angles"], [9, 5, 1, "", "draw_arc"], [9, 5, 1, "", "draw_array"], [9, 5, 1, "", "draw_arrow"], [9, 5, 1, "", "draw_circle"], [9, 5, 1, "", "draw_ellipse"], [9, 5, 1, "", "draw_html"], [9, 5, 1, "", "draw_img"], [9, 5, 1, "", "draw_line"], [9, 5, 1, "", "draw_nodebox"], [9, 5, 1, "", "draw_outline"], [9, 5, 1, "", "draw_rect"], [9, 5, 1, "", "draw_rhombus"], [9, 5, 1, "", "draw_slice"], [9, 5, 1, "", "draw_text"], [9, 5, 1, "", "draw_triangle"], [9, 5, 1, "", "first_value"], [9, 5, 1, "", "get_line_type"], [9, 5, 1, "", "get_xs"], [9, 5, 1, "", "get_ys"], [9, 5, 1, "", "intersects_angles"], [9, 5, 1, "", "intersects_box"], [9, 5, 1, "", "intersects_segment"], [9, 5, 1, "", "split_thru_negative_xaxis"], [9, 5, 1, "", "summary"]], "ete4.smartview.renderer.draw_helpers.Box": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"], [9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.draw_helpers.Padding": [[9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.drawer": [[9, 0, 1, "", "Active"], [9, 0, 1, "", "Drawer"], [9, 0, 1, "", "DrawerAlignCircFaces"], [9, 0, 1, "", "DrawerAlignRectFaces"], [9, 0, 1, "", "DrawerCirc"], [9, 0, 1, "", "DrawerCircFaces"], [9, 0, 1, "", "DrawerRect"], [9, 0, 1, "", "DrawerRectFaces"], [9, 0, 1, "", "Size"], [9, 0, 1, "", "TreeActive"], [9, 5, 1, "", "dist"], [9, 5, 1, "", "drawn_size"], [9, 5, 1, "", "get_asec"], [9, 5, 1, "", "get_drawers"], [9, 5, 1, "", "get_empty_active"], [9, 5, 1, "", "get_rect"], [9, 5, 1, "", "make_box"], [9, 5, 1, "", "safe_string"], [9, 5, 1, "", "stack"]], "ete4.smartview.renderer.drawer.Active": [[9, 3, 1, "", "parents"], [9, 3, 1, "", "results"]], "ete4.smartview.renderer.drawer.Drawer": [[9, 3, 1, "", "COLLAPSE_SIZE"], [9, 3, 1, "", "MIN_SIZE"], [9, 3, 1, "", "NPANELS"], [9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "draw_aligned_headers"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_content"], [9, 1, 1, "", "draw_node"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_active_children"], [9, 1, 1, "", "get_collapsed_node"], [9, 1, 1, "", "get_outline"], [9, 1, 1, "", "get_popup_props"], [9, 1, 1, "", "get_selected_children"], [9, 1, 1, "", "is_fully_collapsed"], [9, 1, 1, "", "on_first_visit"], [9, 1, 1, "", "on_last_visit"]], "ete4.smartview.renderer.drawer.DrawerAlignCircFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerAlignRectFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerCirc": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerCircFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.DrawerRect": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerRectFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.Size": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"]], "ete4.smartview.renderer.drawer.TreeActive": [[9, 3, 1, "", "clades"], [9, 3, 1, "", "nodes"]], "ete4.smartview.renderer.face_positions": [[9, 0, 1, "", "AlignedGrid"], [9, 0, 1, "", "Grid"], [9, 5, 1, "", "make_faces"]], "ete4.smartview.renderer.face_positions.AlignedGrid": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.face_positions.Grid": [[9, 1, 1, "", "add_face"]], "ete4.smartview.renderer.faces": [[9, 0, 1, "", "AlignLinkFace"], [9, 0, 1, "", "AlignmentFace"], [9, 0, 1, "", "ArrowFace"], [9, 0, 1, "", "AttrFace"], [9, 0, 1, "", "CircleFace"], [9, 0, 1, "", "Face"], [9, 0, 1, "", "HTMLFace"], [9, 0, 1, "", "ImgFace"], [9, 0, 1, "", "LegendFace"], [9, 0, 1, "", "OutlineFace"], [9, 0, 1, "", "PieChartFace"], [9, 0, 1, "", "RectFace"], [9, 0, 1, "", "ScaleFace"], [9, 0, 1, "", "SelectedCircleFace"], [9, 0, 1, "", "SelectedFace"], [9, 0, 1, "", "SelectedRectFace"], [9, 0, 1, "", "SeqFace"], [9, 0, 1, "", "SeqMotifFace"], [9, 0, 1, "", "StackedBarFace"], [9, 0, 1, "", "TextFace"]], "ete4.smartview.renderer.faces.AlignLinkFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.AlignmentFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_blocks"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "get_seq"]], "ete4.smartview.renderer.faces.ArrowFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 2, 1, "", "orientation"]], "ete4.smartview.renderer.faces.AttrFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_content"]], "ete4.smartview.renderer.faces.CircleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.Face": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "compute_fsize"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "get_content"], [9, 1, 1, "", "in_aligned_viewport"]], "ete4.smartview.renderer.faces.HTMLFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ImgFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.LegendFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.OutlineFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.PieChartFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_pie"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.RectFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ScaleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SelectedCircleFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedRectFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SeqFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SeqMotifFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_regions"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.faces.StackedBarFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.TextFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.layouts": [[9, 4, 0, "-", "context_layouts"], [9, 4, 0, "-", "default_layouts"], [9, 4, 0, "-", "domain_layouts"], [9, 4, 0, "-", "eggnog6_layouts"], [9, 4, 0, "-", "etecompare_layouts"], [9, 4, 0, "-", "evocell_layouts"], [9, 4, 0, "-", "evol_events_layouts"], [9, 4, 0, "-", "ncbi_taxonomy_layouts"], [9, 4, 0, "-", "phylocloud_egg5_layouts"], [9, 4, 0, "-", "seq_layouts"], [9, 4, 0, "-", "spongilla_layouts"], [9, 4, 0, "-", "staple_layouts"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, 0, 1, "", "LayoutGenomicContext"]], "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_context"], [9, 1, 1, "", "get_tooltip"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, 0, 1, "", "LayoutBranchLength"], [9, 0, 1, "", "LayoutBranchSupport"], [9, 0, 1, "", "LayoutLeafName"], [9, 0, 1, "", "LayoutNumberLeaves"], [9, 0, 1, "", "LayoutOutline"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, 0, 1, "", "LayoutBestName"], [9, 0, 1, "", "LayoutBigg"], [9, 0, 1, "", "LayoutCard"], [9, 0, 1, "", "LayoutCazy"], [9, 0, 1, "", "LayoutEvolEvents"], [9, 0, 1, "", "LayoutKeggEnzyme"], [9, 0, 1, "", "LayoutKeggModule"], [9, 0, 1, "", "LayoutKeggNumber"], [9, 0, 1, "", "LayoutKeggPathway"], [9, 0, 1, "", "LayoutLastCommonAncestor"], [9, 0, 1, "", "LayoutPdb"], [9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutProteinName"], [9, 0, 1, "", "LayoutScientificName"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, 0, 1, "", "LayoutEteDiffDistance"]], "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, 0, 1, "", "LayoutHumanOGs"], [9, 0, 1, "", "LayoutUCSC"], [9, 0, 1, "", "LayoutUCSCtrans"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, 0, 1, "", "LayoutEvolEvents"]], "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, 0, 1, "", "LayoutLastCommonAncestor"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, 5, 1, "", "get_layout_evoltype"], [9, 5, 1, "", "get_layout_gnames"], [9, 5, 1, "", "get_layout_lca_rects"], [9, 5, 1, "", "get_layout_ogs_egg5"], [9, 5, 1, "", "get_layout_sciname"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, 0, 1, "", "LayoutAlignment"]], "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_seq"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, 0, 1, "", "LayoutAutoName"], [9, 0, 1, "", "LayoutCuratedName"], [9, 0, 1, "", "LayoutEukOgs"], [9, 0, 1, "", "LayoutPreferredName"], [9, 0, 1, "", "LayoutSciName"], [9, 0, 1, "", "LayoutSeeds"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, 0, 1, "", "LayoutBarplot"]], "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.nodestyle": [[9, 0, 1, "", "NodeStyle"]], "ete4.smartview.renderer.nodestyle.NodeStyle": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "init"]], "ete4.smartview.renderer.treelayout": [[9, 0, 1, "", "TreeLayout"], [9, 5, 1, "", "cased_name"]], "ete4.smartview.renderer.treelayout.TreeLayout": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.treestyle": [[9, 0, 1, "", "TreeStyle"]], "ete4.smartview.renderer.treestyle.TreeStyle": [[9, 1, 1, "", "__init__"], [9, 2, 1, "", "active_face"], [9, 2, 1, "", "active_face_pos"], [9, 1, 1, "", "add_legend"], [9, 2, 1, "", "aligned_panel_footer"], [9, 2, 1, "", "aligned_panel_header"], [9, 1, 1, "", "get_legend"], [9, 2, 1, "", "selected_face"], [9, 2, 1, "", "selected_face_pos"]], "ete4.treematcher": [[12, 4, 0, "-", "treematcher"]], "ete4.treematcher.treematcher": [[12, 0, 1, "", "TreePattern"], [12, 5, 1, "", "match"], [12, 5, 1, "", "safer_eval"], [12, 5, 1, "", "search"]], "ete4.treematcher.treematcher.TreePattern": [[12, 1, 1, "", "__init__"], [12, 1, 1, "", "match"], [12, 1, 1, "", "search"]]}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "property", "Python property"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "module", "Python module"], "5": ["py", "function", "Python function"], "6": ["py", "exception", "Python exception"]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:property", "3": "py:attribute", "4": "py:module", "5": "py:function", "6": "py:exception"}, "terms": {"": [1, 4, 6, 7, 9, 10, 11, 12, 15, 18, 20], "0": [0, 1, 4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "000000": [16, 20], "0000aa": 20, "0030c1": 16, "008339": 20, "009000": 20, "02": 16, "02x": 20, "046042": 20, "05": 19, "061813": 20, "09": [16, 19], "0f": [9, 16], "0f0f0f": 20, "0x7fa23ab236a0": 9, "1": [1, 4, 5, 6, 7, 9, 10, 11, 12, 15, 17, 18, 19, 20], "10": [0, 1, 8, 9, 16, 18, 19, 20], "100": [1, 11, 16, 19, 20], "1000": [9, 11, 16], "10090": 17, "101": [16, 20], "10395": 11, "105": [11, 16, 20], "106": 16, "106234": 20, "1093": 0, "11": [9, 15, 16, 19], "110": [16, 20], "110769": 20, "117570": 17, "117571": 17, "12": [9, 16, 17, 19, 20], "120": [16, 20], "123": 6, "125": [16, 20], "127": 16, "13": [16, 19], "131567": 17, "1338369": 17, "135135": 11, "14": [17, 20], "1425170": 17, "1437010": 17, "15": [9, 11, 16, 19, 20], "150": [16, 20], "155": [16, 20], "16": [16, 20], "160": [16, 20], "16666666666666666": 16, "1765": 16, "180": 16, "1800": 9, "182035": 20, "183": 20, "19": 16, "190": [16, 20], "191": [16, 20], "1987": 4, "1997": 15, "1_": 19, "2": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "20": [4, 9, 16, 20], "200": [9, 16, 20], "2001": 15, "2007": [7, 15], "2009": 15, "201": [16, 20], "2010": 11, "2011": [7, 15], "2015": 0, "2016": 0, "2021": 16, "2023": 16, "2027025": 11, "204419": 20, "207598": 17, "21": 9, "22": 16, "22default": 16, "24": 16, "25": [16, 20], "250": [16, 20], "255": 20, "2665952": 17, "2665953": 17, "27": [7, 16], "271621": 20, "2759": 17, "279f9009f46bf675e3a890c19191158b": 11, "2813598": 17, "2813599": 17, "284": 16, "29": 16, "2c": 16, "2n": 11, "3": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "30": [16, 20], "300": [16, 20], "300613": 20, "3018035": 17, "303": 16, "314146": 17, "314293": 17, "314295": 17, "32523": 17, "32524": 17, "32525": 17, "33154": 17, "33208": 17, "33213": 17, "333333333333333": 16, "33333333333333337": 16, "3333333333333335": 16, "33511": 17, "351": [16, 20], "370": [16, 20], "376913": 17, "38": 7, "3_": 19, "3abranch": 16, "3aleaf": 16, "3d": 0, "3px": 9, "4": [1, 9, 11, 15, 18, 19, 20], "40": 19, "400": 20, "40000000000003": 16, "40674": 17, "42": 11, "420": [16, 20], "45": [7, 16, 17, 20], "5": [1, 4, 9, 11, 15, 16, 18, 19, 20], "50": [1, 6, 16, 19, 20], "5000": [9, 11, 16], "53": 4, "555": 16, "58": 16, "596401": 20, "5b": 16, "5d": 16, "5px": 9, "6": [1, 7, 9, 11, 16, 19, 20], "60": [9, 16, 20], "600": 20, "6000": 9, "600mb": 17, "6072": 17, "629395": 17, "640858": 20, "65": [4, 16, 20], "6b92d6": 9, "7": [1, 9, 11, 16, 19], "70": [9, 16, 20], "700": 9, "72mb": 17, "753230": 20, "76": 15, "7707": 17, "7711": 17, "7742": 17, "7776": 17, "8": [1, 7, 9, 11, 16, 19, 20], "80": [9, 16], "800": 16, "800000": 9, "8287": 17, "83": 17, "85": [16, 20], "8782": 17, "89593": 17, "8d8d8d": 9, "9": [1, 9, 10, 11, 15, 16, 19], "90": [11, 16, 20], "9347": 17, "9443": 17, "945": 11, "9526": 17, "953250": 20, "9598": 17, "9604": 17, "9605": 17, "9606": 17, "964b00": 16, "973467": 20, "9db0cf": 20, "A": [0, 1, 4, 5, 7, 10, 11, 12, 14, 16, 17, 19, 20], "And": [11, 15, 19, 20], "As": [11, 15, 16, 19], "At": 0, "Being": 19, "But": [18, 19], "By": [1, 4, 7, 15, 16, 19], "For": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "If": [1, 5, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "In": [1, 11, 15, 16, 17, 18, 19, 20], "It": [4, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "Its": [5, 7, 19], "No": 20, "Of": [18, 19], "On": 17, "One": [11, 16, 18, 19, 20], "Or": [16, 17, 19, 20], "Such": 19, "That": 19, "The": [0, 1, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 20], "Then": 11, "There": [1, 11, 15, 18, 19, 20], "These": [16, 17, 19], "To": [8, 11, 15, 16, 17, 19, 20], "Will": [18, 19], "With": [19, 20], "_": [7, 15, 19], "_0_": 19, "_2_": 19, "__init__": [4, 7, 8, 9, 10, 11, 12, 16, 20], "__main__": 20, "__name__": [11, 20], "_get_collaps": 11, "_get_initi": 11, "_get_sm_styl": 11, "_get_styl": 11, "a1": [9, 16, 20], "a2": [9, 16, 20], "a3": [16, 20], "a4": 20, "a50000": 9, "aa": [9, 16, 19], "aa0000": 20, "aaaaaaaaaaa": 8, "ab": [4, 16, 19], "abc": 6, "abc_layout": 20, "abcd": 19, "abcdefghijklmnopqrstuvwxyz": 5, "abl": [1, 16, 18, 19], "abort": 9, "about": [2, 7, 9, 15, 16, 18, 19, 20], "abov": [15, 16, 17, 19, 20], "absolut": [11, 15], "accept": [6, 11, 16, 17, 18, 19, 20], "access": [7, 15, 16, 17, 19, 20], "accord": [5, 6, 7, 9, 11, 15, 19, 20], "accur": 0, "acept": 4, "across": 1, "act": [16, 20], "action": [16, 19], "activ": [9, 16], "activate_clad": 9, "activate_nod": 9, "active_children": 9, "active_fac": 9, "active_face_po": 9, "active_layout": 9, "active_nod": 9, "actual": [1, 19], "acycl": 19, "ad": [7, 10, 11, 14, 16, 17, 19, 20], "adapt": [16, 17], "add": [1, 4, 5, 7, 8, 9, 10, 11, 17, 19], "add_branch_valu": [3, 5], "add_child": [11, 19], "add_children": 11, "add_fac": [9, 11, 16, 20], "add_face_smartview": 11, "add_face_to_nod": [1, 20], "add_face_treeview": 11, "add_featur": 11, "add_leaf_nam": [3, 5], "add_legend": [9, 16], "add_next_branch": 5, "add_prop": [11, 16, 17, 19, 20], "add_sist": [11, 19], "add_tre": 9, "add_trees_from_request": 9, "addit": [16, 17, 18, 19], "addition": [15, 19], "adh1": 19, "adh2": 19, "adh3": 19, "adh4": 19, "adhi": 19, "adhx": 19, "adjac": 20, "adjust": [15, 16, 20], "adress": 11, "advance_layout": 16, "advantag": [16, 20], "aeiou": 19, "affect": [10, 15, 19, 20], "after": [6, 7, 11, 15, 16, 19, 20], "ag": [7, 15], "again": [1, 15, 18, 19], "age2nam": 15, "agp": 0, "ahtpssldtphfvfqtykmgapplppstaapvgqgarqddssssaspsvqgaprevvdpsggwatllesir": [16, 20], "aid": 4, "aim": 15, "ajmonlin": 11, "al": 15, "alg": 15, "alg_format": [7, 15], "algorithm": [7, 16, 19], "alia": 9, "align": [0, 2, 3, 7, 9, 11, 14, 20], "aligned_fac": [9, 16], "aligned_panel_foot": [9, 16], "aligned_panel_head": [9, 16], "alignedgrid": 9, "alignlinkfac": 9, "alignmentfac": [9, 16], "all": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 20], "all_act": 16, "all_select": 16, "allow": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "almost": 1, "aln": 16, "along": 19, "alqeklkdfpvcvstkpepeddaeeglgglpsn": [16, 20], "alreadi": [17, 18, 19, 20], "also": [4, 7, 9, 10, 11, 15, 17, 18, 19, 20], "altern": [8, 10, 15, 19], "although": [15, 16, 19, 20], "altnvsh": 15, "altnvshnia": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeah": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "altnvshniavqylsefgtddqpdrreeah": 15, "alwai": [11, 15, 18, 19], "amniota": 17, "among": [11, 15, 16, 19], "an": [5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "analogi": 19, "analys": [0, 15, 19, 20], "analysi": [0, 4, 15, 16, 19, 20], "analyz": [4, 19], "ancestor": [5, 9, 10, 11, 16], "ancestor_a": 16, "ancestor_b": 16, "ancestor_c": 16, "ancestor_d": 16, "ancestor_jfc": 19, "ancestr": 15, "anchor": 9, "anchor_stroke_color": 9, "anchor_stroke_width": 9, "ancylobact": 17, "angl": 9, "ani": [1, 5, 6, 9, 10, 11, 15, 16, 17, 18, 19, 20], "annot": [0, 7, 10, 14], "annotate_dict": 17, "annotate_gtdb_taxa": [7, 17], "annotate_ncbi_taxa": [7, 17], "annotate_tre": 10, "annular": 9, "anoth": [10, 11, 16, 19], "answer": 17, "ap": 20, "apart": 20, "aperlqeygsiftda": [16, 20], "api": [0, 9], "app": 9, "appear": [9, 11, 15, 16, 19], "append": [16, 19], "appl": 4, "appli": [15, 16, 17, 19, 20], "applic": 15, "apply_transl": 6, "approach": [15, 17, 19], "appropri": [9, 12, 15], "aqak": [16, 20], "aquaticu": 17, "ar": [4, 7, 8, 10, 11, 12, 15, 16, 17, 18, 19, 20], "arbitrari": [5, 11, 18, 20], "arbitrarili": 19, "arc": 9, "arc_span": 20, "arc_start": 20, "arc_typ": 9, "area": [16, 20], "arg": [6, 9, 20], "argument": [4, 6, 7, 10, 15, 16, 19, 20], "arial": [16, 20], "around": [16, 20], "arrai": [4, 9, 11, 16], "arrayt": 4, "arraytbl": 4, "arrow": 9, "arrow_typ": 9, "arrowfac": 9, "ascii": 11, "asec": 9, "ask": [2, 15], "aspect": 14, "assert_root_consist": [3, 5], "assertionerror": 5, "assign": [7, 9, 11, 15, 17], "assist": [15, 19], "associ": [0, 4, 7, 8, 10, 11, 15, 17], "assum": [1, 7, 19], "attach": [11, 15, 16, 20], "attempt": 17, "attr": 9, "attrfac": [1, 9, 20], "attribut": [9, 10, 11, 14, 15, 16, 17, 20], "attributt": 16, "auto": 9, "autodetect": 15, "autodetect_dupl": [7, 15], "autom": [0, 19], "automat": [1, 7, 9, 11, 14, 18, 19, 20], "av": 17, "avail": [7, 9, 11, 15, 16, 19, 20], "averag": 19, "avocado": 0, "avoid": [7, 8, 16, 19], "avrilom": 0, "awar": [0, 15], "b": [1, 4, 5, 11, 16, 17, 18, 19, 20], "b1": [9, 16, 20], "b2": [9, 16, 20], "b3": [16, 20], "b4": [16, 20], "backbon": 16, "background": 15, "bacpathgenom": 0, "bacteria": 17, "bacteriovorax": 17, "bacteriovoru": 17, "balanc": [7, 11, 19], "bar": [6, 9], "barcelona": 0, "barplot": 16, "barplot_layout": 16, "basal": 19, "base": [4, 7, 9, 11, 15, 17, 19, 20], "basic": [1, 7, 14, 15, 16, 20], "bcc3d0": [9, 16], "bda": 9, "bda0": 9, "bda1": 9, "bdellovibrio": 17, "bdellovibrionota": 17, "bdr": 9, "bdx": 9, "bdy": 9, "bdy0": 9, "bdy1": 9, "becaus": [15, 16], "becom": 19, "been": [4, 15], "befor": [11, 16, 18, 19, 20], "beforehand": 18, "begin": 19, "behavior": 15, "behind": 11, "being": [11, 15, 19], "belong": [15, 20], "below": [16, 19, 20], "benefit": 15, "besid": 15, "best": [9, 10, 15, 18, 20], "best_nam": 9, "better": [7, 19], "between": [5, 7, 11, 14, 15, 16], "bf": 11, "bgcolor": [9, 16, 20], "bifurc": 19, "bigg": 9, "bigger": 16, "biggest": 5, "bilateria": 17, "binari": 11, "bio": 11, "bioinformat": [0, 7, 19], "biol": [0, 7], "biologi": [0, 15], "biped": 20, "black": [9, 16, 19, 20], "blank": [16, 20], "blog": 0, "blue": [9, 16, 20], "bold": 20, "bool": [7, 9, 11], "boolean": 19, "bootstrap": 19, "border": [16, 20], "boreoeutheria": 17, "bork": 0, "both": [11, 15, 16, 19, 20], "bottl": 16, "bottom": [11, 16, 20], "bottom_textfac": 16, "bottommost": 19, "bound": 9, "boundingrect": 20, "box": [9, 16], "box1": 9, "box2": 9, "box_motif": [16, 20], "bprop": [5, 11], "bracket": 19, "branch": [5, 9, 10, 11, 14, 15], "branch_bottom": [9, 11, 16], "branch_right": [9, 11, 16], "branch_top": [9, 11, 16], "branch_vertical_margin": 20, "breadth": [5, 11], "break": 20, "brief": 0, "brother": 19, "brown": [16, 20], "brows": [2, 14], "browser": [9, 16], "btext": 9, "bubble_map": 20, "build": [0, 9], "build_block": 9, "build_region": 9, "built": [15, 16, 19, 20], "bunch": 11, "button": 16, "bye": 18, "c": [1, 4, 5, 11, 16, 18, 19, 20], "c1": [16, 20], "c2": [16, 20], "c3": [16, 20], "c43b5d": 9, "c__korarchaeia": 17, "c__peptococcia": 17, "cach": [11, 14, 18], "cached_cont": [7, 11], "calcul": [4, 7, 10, 11, 15, 19], "call": [1, 9, 11, 12, 15, 16, 17, 18, 19, 20], "callback": 9, "can": [4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "cani": [15, 20], "canida": 20, "cannot": 19, "cansnper": 0, "card": 9, "care": 19, "cartesian": 9, "cascad": 11, "case": [1, 11, 15, 16, 19, 20], "cased_nam": 9, "catarrhini": 17, "categori": 15, "cazi": 9, "cbgp": 0, "cccccc": 20, "cd": 19, "cellular": 17, "center": [5, 9, 20], "centroid": 4, "cepa": [0, 7, 15], "certain": [15, 19], "cfa": [15, 20], "cfa_001": 15, "ch": [16, 18], "chang": [1, 5, 6, 11, 15, 16, 18, 19], "change_selection_nam": 9, "char": [5, 8], "charact": [6, 15], "charleston": 15, "check": [1, 11, 14, 15, 16, 18, 20], "check_interv": 9, "check_monophyli": [11, 19], "child": [5, 7, 10, 11, 19], "child_idx": 11, "child_po": 5, "children": [4, 5, 7, 9, 11, 12, 16, 18, 19, 20], "chimp": [15, 20], "chimp_1": 15, "chimp_2": 15, "chimp_3": 15, "chimpa": 15, "chimpanze": 20, "chimpb": 15, "chimpc": 15, "chimpfac": 20, "choos": [16, 20], "chordata": 17, "chosen": 7, "cipf": 0, "circ": 9, "circl": [9, 16, 20], "circle_typ": 9, "circlefac": [9, 16, 20], "circular": [9, 16, 19], "circular_styl": 20, "circumasec": 9, "circumfer": 20, "circumrect": 9, "circumscrib": 9, "citat": [0, 4, 7, 17], "citrobact": 16, "clade": [9, 17], "clade_typ": 11, "class": [2, 3, 4, 5, 7, 8, 9, 10, 12, 15, 16, 17, 18, 19, 20], "classif": [0, 17], "classifi": 0, "click": 16, "climateecologi": 0, "clip": [16, 20], "clip_angl": 9, "clock": 20, "clonal": 0, "clone": [11, 19], "closest": 11, "cluster": [2, 3, 19], "clustertre": [3, 4], "code": [1, 5, 7, 9, 11, 12, 15, 16, 17, 19, 20], "code2desc": 20, "code2nam": [15, 20], "col": [9, 20], "collaps": [7, 9, 10, 11], "collapse_by_conserv": 9, "collapse_conserv": 9, "collapse_lineage_specific_expans": [7, 15], "collapse_s": [9, 16], "collapse_subspeci": [10, 17], "collapsed_fac": 11, "collapsed_id": [9, 16], "collapsed_leaf": 19, "collapsed_nod": 9, "collapsed_onli": [9, 11, 16], "collapsing_height": 9, "collect": [5, 8, 11, 16, 19, 20], "colloqui": 20, "color": [9, 19, 20], "color_gradi": [9, 16], "color_prop": 9, "color_rang": [9, 16], "colormap": [9, 16], "colorsi": 20, "colorstrip": 16, "column": [1, 9, 11, 16, 20], "com": [0, 11, 16, 17], "combin": [11, 14, 15, 17], "combinatori": 15, "combinedlayout_bas": 16, "combinedlayout_object": 16, "comfort": 18, "command": [6, 9, 16, 19], "comment": [6, 8], "common": [5, 7, 9, 10, 11, 15, 16, 18, 20], "common_ancestor": [3, 5, 11, 15, 16, 19, 20], "common_edg": 19, "commonli": [17, 19], "compact": [11, 18, 19], "compact_aln": 16, "compactseq": [16, 20], "compar": [0, 11, 14, 15], "comparison": [0, 15, 19], "compars": 0, "compat": [7, 11, 19], "compil": 18, "complet": [10, 15, 16, 19, 20], "complex": [11, 16, 18, 19], "compon": 16, "comprehens": [17, 19], "compress": [9, 11], "compris": 19, "comput": [0, 4, 9, 11, 19], "compute_bounding_box": 9, "compute_fs": 9, "compute_pi": 9, "concaten": 14, "concept": 19, "conceptu": 19, "condit": [11, 12, 16, 18, 19], "conf": 19, "confer": 0, "confid": 19, "config": [16, 20], "connect": [10, 11, 17, 19], "connector": 10, "conost": 16, "conostant_color": 16, "conostant_node_s": 16, "conostant_textfac": 16, "consequ": 15, "conserv": 11, "conservation_threshold": 9, "consid": [11, 15, 19], "consider": 19, "consist": [11, 16, 17, 19], "consol": 18, "constant": 19, "constraint": 12, "construct": [18, 19], "constructor": [12, 19, 20], "contact": 0, "contain": [7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "container_typ": 11, "content": [4, 6, 7, 11, 14], "content_repr": 6, "content_s": 9, "context": [12, 16, 18], "continu": [16, 20], "contrast": 19, "control": [19, 20], "conveni": [15, 17, 19], "convent": [5, 11, 19], "convers": [17, 20], "convert": [1, 5, 7, 10, 11, 15, 17, 19], "cool": 19, "cophenet": 11, "cophenetic_matrix": 11, "copi": [7, 11, 14, 20], "copy_styl": 9, "copyright": 16, "core": [9, 11, 15], "corner": 16, "correct_by_polytomy_s": 11, "correspond": [5, 6, 7, 9, 10, 15, 18, 19, 20], "correspondig": 15, "could": [1, 4, 11, 15, 16, 18, 19, 20], "count": [16, 19], "count_leav": 9, "courier": 16, "cours": [18, 19], "cover": 7, "cpickl": [11, 19], "craniata": 17, "creat": [1, 4, 5, 9, 11, 12, 15, 16], "create_dichotomic_sist": [3, 5], "credit": 16, "crg": 0, "criteria": [7, 11], "crucial": 19, "cryptofilum": 17, "ctrl": 16, "current": [1, 5, 7, 8, 9, 10, 11, 15, 16, 19], "cursor": 16, "custom": [1, 10, 11, 14, 17], "cut": [9, 11, 19], "cyprinida": 20, "d": [1, 4, 5, 7, 9, 11, 15, 16, 18, 19, 20], "d0d0d0": 9, "d1": 16, "d2": 16, "d__archaea": 17, "d__bacteria": 17, "da": 9, "daili": 17, "danio": 20, "darkr": [16, 20], "darkseagreen": [16, 20], "darwin": 11, "dash": [9, 16, 20], "data": [0, 4, 9, 11, 15, 16, 17, 19, 20], "databas": [0, 2, 3, 7, 14], "date": 14, "dbfile": [7, 10], "deactiv": 16, "deactivate_clad": 9, "deactivate_nod": 9, "deal": [15, 19], "decid": [16, 19], "deepcopi": [11, 19], "deepest": 19, "def": [1, 7, 15, 16, 19, 20], "default": [1, 4, 6, 7, 11, 15, 16, 17, 19, 20], "defin": [9, 15, 17, 18, 19, 20], "definit": 19, "del_featur": 11, "del_prop": [11, 19], "del_tre": 9, "delet": [9, 11], "delete_orphan": 11, "delimit": 0, "demonstr": 16, "dendrochirotida": 17, "dendrogram": 5, "dengzq1234": 16, "denisova": 17, "depart": 0, "depend": [1, 5, 11, 15, 19, 20], "depth": [11, 19], "deriv": [10, 20], "descend": [4, 5, 7, 10, 11, 14, 16, 18], "descfac": 20, "describ": [7, 11, 15, 16, 18], "descript": [1, 4, 9, 11, 16, 19, 20], "design": [19, 20], "detach": 11, "detail": [7, 19, 20], "detect": [1, 7, 11, 14, 17, 19], "determin": [19, 20], "deuterostomia": 17, "develop": 0, "deviat": 4, "df": 11, "diamet": [4, 5, 16, 20], "dichotom": [5, 11], "dichotomi": 5, "dicotom": [5, 11], "dicotomi": [5, 11], "dict": [4, 6, 9, 10, 11, 16], "dictionari": [7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "did": [18, 19], "diff": 9, "diff_node_color": 9, "diff_node_s": 9, "differ": [1, 7, 9, 11, 14, 15, 16, 18, 19, 20], "differenti": 19, "digit": 16, "dimension": 11, "dipnotetrapodomorpha": 17, "diptera": 20, "direct": 15, "directli": [16, 19, 20], "disabl": [15, 19], "discard": 19, "discarded_edges_t1": 11, "discarded_edges_t2": 11, "disconnect": 19, "discret": [9, 16], "displai": 0, "dist": [5, 6, 9, 11, 16, 18, 19, 20], "dist_fn": [5, 11], "distanc": [1, 4, 5, 9, 11, 14, 15], "distant": [15, 19], "distinct": 19, "distinguish": 18, "distribut": 17, "diverg": 15, "divid": 11, "dme": [15, 20], "dme_001": 15, "dme_002": 15, "dmp": 17, "do": [5, 11, 12, 15, 16, 18, 19, 20], "doc": 20, "document": [15, 16, 20], "doe": [1, 10, 12, 15, 17, 18, 19, 20], "doesn": [17, 18], "dog": [15, 20], "dogfac": 20, "doi": 0, "domain_layout": 16, "domest": 20, "don": 5, "done": [6, 15, 16, 19], "dopazo": 7, "dot": [9, 11, 16, 20], "doubl": 11, "down": 19, "download": [10, 15, 17], "downward": 19, "dpi": [11, 20], "draw": [2, 11, 14, 15], "draw_aligned_head": 9, "draw_arc": 9, "draw_arrai": 9, "draw_arrow": 9, "draw_childrenlin": 9, "draw_circl": 9, "draw_collaps": 9, "draw_cont": 9, "draw_descend": [9, 16], "draw_ellips": 9, "draw_html": 9, "draw_img": 9, "draw_lengthlin": 9, "draw_lin": 9, "draw_nod": 9, "draw_nodebox": 9, "draw_nodedot": 9, "draw_outlin": 9, "draw_rect": 9, "draw_rhombu": 9, "draw_slic": 9, "draw_text": [9, 16], "draw_triangl": 9, "drawer": 16, "draweraligncircfac": 9, "draweralignrectfac": 9, "drawercirc": 9, "drawercircfac": 9, "drawerrect": 9, "drawerrectfac": 9, "drawn": [16, 20], "drawn_siz": 9, "dre": 20, "drosophila": [15, 20], "dump": [6, 10, 15, 17], "dunn": 4, "dup": [7, 15], "dup1": 15, "dup2": 15, "dup3": 15, "duplic": [0, 1, 7, 11, 14], "duplication_color": 9, "dure": [16, 20], "dx": [9, 16], "dx_befor": 9, "dx_to_closest_child": 9, "dy": [9, 16], "dy_befor": 9, "dynam": [7, 11, 15, 16, 19, 20], "dynamicitemfac": 20, "e": [0, 1, 5, 9, 10, 11, 16, 18, 19, 20], "e5e5e5": 16, "each": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "easier": 17, "easiest": [1, 17], "easili": [15, 17, 19, 20], "edg": [11, 16, 19], "edges_t1": 11, "edges_t2": 11, "edit": 16, "editor": 16, "ef": [15, 19], "effect": [8, 11], "effective_tree_s": 19, "effici": [15, 17, 18], "efg": 19, "efgdlnealnsi": 15, "efgdlnealnsyyayqtddqkdrreeah": 15, "efgdlnealnsyyayqtddqkdrreeahqfmaltnvsh": 15, "efgtddqkdrreeah": 15, "eggnog": 0, "either": [9, 17, 19], "element": [1, 9, 11, 16, 19, 20], "elif": [15, 16, 20], "ellips": 20, "ellipse_typ": 9, "els": [1, 16, 17, 19, 20], "embl": 0, "emploi": 17, "empti": [4, 11, 15, 17, 19, 20], "emul": 19, "enabl": [1, 16], "enclos": 19, "encod": [7, 8, 11, 15, 19], "end": [1, 6, 9, 11, 16, 18, 19, 20], "engin": [1, 15, 16, 20], "enhanc": 16, "enjoi": 18, "enorm": 15, "ensur": [16, 20], "entail": 19, "entir": [16, 19], "entiti": 17, "entri": 8, "enumer": 20, "environ": 16, "environment": 17, "enzym": 9, "equal": [16, 19, 20], "equidist": [5, 11, 16], "error": [6, 9, 11, 18], "escap": 6, "escaped_char": 6, "escherichia": 16, "essenti": [16, 17, 19], "establish": [15, 19], "estim": [7, 20], "et": [9, 10, 11, 14, 15, 16, 17, 18, 20], "etc": [11, 16, 18, 20], "ete3": [0, 16], "ete4": [1, 9, 11, 14, 15, 16, 18, 19, 20], "ete4_galleri": 16, "etetoolkit": [0, 17], "etiqqfmaltnvshniavqylsefgdln": 15, "etyp": [7, 15], "euarchontoglir": 17, "euclidean": 4, "euk": 9, "eukaryota": 17, "eumetazoa": 17, "euteleostomi": 17, "eutheria": 17, "ev": 15, "eval": [9, 12, 16], "evalu": [9, 16, 18], "even": [11, 15, 16, 17, 19, 20], "event": [7, 9, 14], "event1": 15, "event2": 15, "everi": [5, 9, 11, 15, 16, 19], "everywher": 9, "evol": 0, "evolev": [3, 15], "evoltyp": [7, 15], "evolutionari": [7, 9, 14, 19], "exact": [5, 10, 15, 19], "exactli": 11, "examin": 19, "exampl": [0, 1, 4, 5, 6, 7, 8, 9, 11, 14, 15, 17, 19, 20], "except": [6, 18, 19], "exclud": [11, 19], "exclude_prop": [9, 11, 16], "exclus": [11, 19], "execut": [16, 20], "exist": [18, 19], "exit": 11, "expand": [11, 19], "expand_polytomi": 11, "expans": [7, 15], "expect": [4, 7, 15, 18, 19], "expected_result": 18, "experi": 1, "experiment": 10, "explain": 15, "explanatori": 19, "explor": [0, 1, 2, 9, 11, 14, 15, 19, 20], "explore_show": 16, "explore_standalon": 16, "exponenti": 11, "export": [19, 20], "express": [9, 12, 14], "extant": 20, "extend": [7, 9, 11, 15, 19], "extens": [1, 11, 15, 20], "extern": [16, 19, 20], "extra": [9, 16, 18, 19, 20], "extract": [6, 9, 17], "extrem": 1, "f": [1, 5, 11, 15, 16, 18, 19, 20], "f__korarchaeacea": 17, "f__tho": 17, "f__thorarchaeacea": 17, "fa8072": 9, "faa": 16, "face": [1, 3, 11, 14], "face1": 9, "face2": 9, "face_grid_tutori": 20, "facecontain": 9, "faceposition_al": 16, "faceposition_align": 16, "faceposition_bottom": 16, "faceposition_collaps": 16, "faceproperties_textfac": 16, "facilit": [17, 19], "fact": 19, "fade": 16, "fals": [1, 5, 7, 9, 10, 11, 12, 15, 16, 19, 20], "famili": [7, 11, 14, 17, 20], "familiar": 19, "familiari": [15, 20], "fanci": 1, "farthest": [3, 5, 7, 11, 15, 19], "farthest_descend": [3, 5], "fast": [0, 19], "fasta": [7, 8, 15, 16], "fasta_txt": 15, "fastafil": 16, "faster": [14, 15], "fb3640": 9, "fdist": 4, "feasibl": 11, "featur": [0, 1, 4, 7, 11, 15, 16, 17, 19, 20], "feel": 18, "fetch": 17, "few": [15, 18], "ff0000": [16, 20], "fgcolor": [9, 16, 20], "field": [9, 16], "file": [1, 4, 6, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "file_nam": 11, "filenam": [1, 9], "fileobject": 9, "filter": [15, 19], "final": [18, 19, 20], "find": [5, 11, 15, 16, 18], "find_nod": 9, "fine": [4, 11], "fir": 15, "first": [5, 7, 9, 10, 11, 15, 16, 17, 18, 20], "first_valu": 9, "first_visit": 5, "fish": [15, 20], "fish_1": 15, "fish_3": 15, "fishfac": 20, "fit": 9, "fix": [11, 15], "fix_dupl": 8, "flag": [11, 15, 19], "flexibl": [1, 19], "fli": 20, "float": [9, 11, 16, 20], "flush_outlin": 9, "fly": [15, 16, 20], "flyfac": 20, "fma": 15, "fmaltnvsh": 15, "fmaltnvshniavqi": 15, "fn": [4, 7], "fname": 17, "fo": 16, "follow": [1, 4, 7, 11, 15, 16, 17, 19, 20], "font": 1, "foo": 6, "footer": [9, 16], "forc": 8, "force_topologi": 1, "foreground": [16, 20], "form": [9, 11, 16], "formal": 19, "format": [4, 6, 7, 8, 9, 10, 11, 15, 17, 19, 20], "format_root_nod": [6, 7, 11], "formatt": [9, 16], "forward": 20, "fould": 11, "found": [4, 7, 15, 16, 18, 19, 20], "foundat": 16, "four": [16, 20], "fp": 6, "frame": 16, "framework": 16, "francoi": 0, "free": [0, 18], "freeli": [18, 19], "frequenc": 16, "frequent": [2, 19], "freshwat": 20, "from": [1, 5, 6, 7, 9, 10, 11, 14, 15, 16, 17, 20], "from_parent_child_t": 11, "from_skbio": 11, "from_skibio": 11, "front": [9, 11], "fseq": 15, "fsize": [1, 20], "ftp": 17, "ftype": [9, 16], "full": [6, 11, 15, 16, 19], "fullfil": 17, "fulli": [16, 17, 20], "function": [1, 4, 5, 7, 9, 11, 15, 17, 18], "fundament": 16, "fungi": 19, "further": 17, "futher": 16, "futur": [5, 11, 17], "g": [1, 6, 11, 16, 18, 19, 20], "g9": 17, "g__b65": 17, "g__jacael01": 17, "g__korarchaeum": 17, "g__mp8t": 17, "g__owc5": 17, "g__shmx01": 17, "g__smtz1": 17, "g__tekir": 17, "g__wtck01": 17, "gabaldon": [7, 15], "gap_format": [9, 16, 20], "gap_linewidth": [9, 16], "gapcolor": [9, 16, 20], "gb_gca_003344655": 17, "gb_gca_003662765": 17, "gb_gca_003662805": 17, "gb_gca_013138615": 17, "gb_gca_020833055": 17, "gdlneal": 15, "gdlnealnsi": 15, "gene": [7, 9, 11, 14], "gene_nam": 9, "gene_tree_nw": 15, "gener": [2, 5, 11, 15, 16, 19, 20], "genes_tre": 19, "genet": 17, "genetre": 15, "genom": [0, 7, 9, 15, 17], "genotyp": 0, "genu": [17, 20], "geometr": [16, 20], "germani": 0, "get": [7, 9, 10, 14, 15, 16, 18], "get_active_children": 9, "get_active_clad": 9, "get_ag": [7, 15], "get_age_balanced_outgroup": 7, "get_asec": 9, "get_background": 16, "get_box": 9, "get_broken_branch": 10, "get_cached_cont": [11, 18, 19], "get_children": 11, "get_closest_leaf": 11, "get_collapsed_nod": 9, "get_color": 9, "get_command": 6, "get_command_search": 9, "get_common_nam": 10, "get_cont": 9, "get_context": 9, "get_descendant_evol_ev": [7, 15], "get_descendant_taxa": [10, 17], "get_descendants_evol_ev": 7, "get_dist": [11, 19], "get_draw": 9, "get_dunn": 4, "get_empty_act": 9, "get_entri": 8, "get_eval_search": 9, "get_example_tre": 20, "get_extended_prop": 6, "get_farthest_leaf": [11, 19], "get_farthest_nod": [11, 19], "get_farthest_oldest_leaf": [7, 15], "get_farthest_oldest_nod": [7, 15], "get_fuzzy_name_transl": 10, "get_heatmapfac": 16, "get_i": 9, "get_layout": 9, "get_layout_evoltyp": 9, "get_layout_gnam": 9, "get_layout_lca_rect": 9, "get_layout_ogs_egg5": 9, "get_layout_scinam": 9, "get_layouts_from_gett": 9, "get_legend": 9, "get_line_typ": 9, "get_lineag": [10, 17], "get_lineage_transl": 10, "get_midpoint_outgroup": [11, 19], "get_monophylet": [11, 19], "get_my_evol_ev": [7, 15], "get_name_lineag": 10, "get_name_transl": [10, 17], "get_newick": 9, "get_next_available_port": 9, "get_node_fac": 16, "get_nodes_info": 9, "get_outlin": 9, "get_par": 9, "get_pars": 9, "get_popup_prop": 9, "get_prop": [6, 11], "get_rank": [10, 17], "get_rect": 9, "get_search_funct": 9, "get_sect": 6, "get_select": 9, "get_selected_children": 9, "get_selection_info": 9, "get_seq": [8, 9, 16], "get_silhouett": 4, "get_sist": 11, "get_speci": [7, 15], "get_speciation_tre": [7, 15], "get_species_nam": 15, "get_stat": 9, "get_taxid_transl": [10, 17], "get_tid": 9, "get_tooltip": 9, "get_topologi": [10, 17], "get_topological_search": 9, "get_topology_id": 11, "get_tre": 6, "get_tree_styl": 16, "get_trees_from_fil": 9, "get_trees_from_form": 9, "get_trees_from_nexus_or_newick": 9, "get_x": 9, "getattr": 18, "gist": 11, "github": [11, 16, 17], "given": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 20], "global": 9, "globalstuff": 9, "glqrrprhriqsk": [16, 20], "gmail": 0, "gnathostomata": 17, "go": [11, 18, 19], "go_back": 5, "goal": 1, "goe": 16, "gold": [16, 20], "googlegroup": 0, "gracefulli": 9, "gradient": 15, "gradient_color": 16, "grai": [9, 16, 20], "grain": [4, 11], "graph": [16, 19, 20], "graphic": [2, 3, 4, 16, 19, 20], "gray_aln": 16, "great": 11, "greatli": 0, "green": [16, 19, 20], "grei": 9, "grid": 9, "group": [0, 7, 10, 11, 15, 19], "grow": [5, 11, 19], "gtdb": [10, 14], "gtdb202dump": 17, "gtdb_spcode": 17, "gtdb_taxonomi": 17, "gtdb_to_taxdump": 17, "gtdbtaxa": [3, 17], "gtdbtaxdump": 10, "gui": [16, 19, 20], "guid": [0, 2], "gz": [10, 17], "h": [1, 7, 11, 15, 16, 18, 19, 20], "ha": [5, 6, 9, 11, 15, 16, 18, 19], "halter": 20, "hampshir": [11, 19], "hand": 17, "handi": 19, "handl": [0, 19, 20], "hang": [5, 11, 19], "haplorrhini": 17, "hard": [5, 11], "has_dupl": 11, "has_unvisited_branch": 5, "have": [5, 10, 11, 15, 16, 18, 19], "head": 16, "header": [9, 11, 16], "heatmap": 20, "heidelberg": 0, "heidelbergensi": 17, "height": [9, 11, 16, 19, 20], "hello": [16, 18, 20], "help": [16, 17], "henc": 16, "here": [15, 16, 17, 19, 20], "hex": 16, "hide": 20, "hierarch": [10, 11, 19, 20], "high": 19, "higher": 19, "highli": [16, 20], "highlight": [2, 16, 20], "hind": 20, "histori": 16, "hit": 16, "hls_to_rgb": 20, "hniavqylsefgdln": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeah": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqf": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqfmaltnvshqfmaltnvsh": 15, "hniavqylsefgtddikdrreeah": 15, "hola": [16, 20], "hold": 19, "holt": 0, "home": [4, 11], "hominid": 15, "hominida": [17, 20], "hominina": 17, "hominoidea": 17, "homo": [15, 16, 17, 20], "homolog": 15, "hook": [16, 20], "hop": 11, "horizont": [9, 16], "host": [9, 11], "houben": 15, "hover": 16, "hoverenterev": 20, "hoverleaveev": 20, "how": [0, 4, 11, 15, 16, 18, 20], "howev": [1, 15, 17, 19, 20], "hsa": [15, 20], "hsa_001": 15, "hsa_002": 15, "hsa_003": 15, "hsa_004": 15, "html": [1, 9], "html_type": 9, "htmlface": 9, "http": [1, 11, 16, 17, 19], "hue": 20, "huerta": [0, 7, 15], "human": [7, 9, 11, 15, 19, 20], "human_1": 15, "human_2": 15, "human_3": 15, "human_orth": 9, "human_orth_prop": 9, "human_seq": 15, "humana": 15, "humanb": 15, "humanc": 15, "humand": 15, "humanfac": 20, "hundr": 15, "hz_line_color": [16, 20], "hz_line_typ": [16, 20], "hz_line_width": [9, 16, 20], "i": [0, 4, 5, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "id": [9, 11, 16, 19], "idea": [9, 11, 18, 19], "identifi": [7, 9, 15, 17], "idx": 9, "ignor": [15, 17], "ikgskkaikvfssa": [16, 20], "imag": [11, 14, 16], "imagin": 18, "img": 9, "img_fac": 20, "img_path": [9, 20], "img_styl": [11, 20], "img_typ": 9, "imgfac": [9, 20], "implement": [1, 7, 19, 20], "import": [1, 5, 11, 15, 16, 17, 18, 19, 20], "impos": 18, "improv": [0, 15], "in_aligned_viewport": 9, "in_seq": [7, 15], "in_viewport": 9, "inch": [11, 20], "includ": [1, 5, 7, 8, 15, 16, 17, 18, 19, 20], "include_prop": [9, 11, 16], "include_root": 11, "inconsist": 5, "incorpor": 19, "incorrect": 18, "increas": 20, "inde": 19, "independ": [11, 16, 19, 20], "index": [2, 4, 5], "individu": 16, "infer": [7, 15, 17, 19], "info": [9, 11, 20], "inform": [7, 9, 11, 14, 16, 19, 20], "inherit": [9, 16], "init": 9, "init_from_et": 11, "init_from_newick": 11, "initi": [7, 9, 15, 16, 20], "initialize_tree_styl": 9, "inner": 19, "inner_bord": 20, "inparalog": 15, "input": [16, 17, 19], "insect": [19, 20], "insensit": 16, "insert": 5, "insert_intermedi": [3, 5], "insid": [16, 18], "instad": [7, 11], "instal": 20, "instanc": [1, 7, 10, 11, 15, 16, 17, 19, 20], "instantan": 19, "instead": [5, 11, 18, 19, 20], "int": [6, 9, 20], "intact": 19, "integ": 11, "integr": [16, 17, 20], "inter": 4, "interact": [11, 14], "interactiveitem": 20, "interchang": 5, "interchange_refer": [3, 5], "interclust": 4, "intercluster_dist": 4, "interest": [15, 19], "interfac": [16, 20], "interior": [5, 11], "interleav": [7, 8], "intermedi": [5, 11, 17], "intermediate_nod": [10, 17], "intern": [5, 7, 9, 10, 11, 15, 17, 19, 20], "internal_1": 19, "internal_2": 19, "internet": 17, "interpol": 16, "interpret": [4, 9, 11, 15, 16, 19], "interrupt": [16, 20], "intersect": 9, "intersects_angl": 9, "intersects_box": 9, "intersects_seg": 9, "intra": 4, "intraclust": 4, "intracluster_dist": 4, "intric": 19, "introduc": [16, 17], "introduct": 0, "invok": 20, "involv": [7, 15, 19], "iphylip": [7, 8, 15], "iphylip_relax": 8, "iphylip_txt": 15, "ipython": 16, "iq": 0, "is_collaps": 11, "is_fully_collaps": 9, "is_initi": 11, "is_leaf": [1, 6, 11, 16, 18, 19, 20], "is_leaf_fn": [5, 6, 7, 11, 19], "is_monophylet": 11, "is_root": [11, 16, 18, 19], "is_smal": 9, "is_vowel": 19, "issvsslllfnttenlykkyvfldplag": [16, 20], "item": [8, 9, 10, 11, 17, 19, 20], "itemfac": 20, "itep": 0, "iter": [5, 7, 8, 11, 18], "iter_entri": 8, "iter_prepostord": 11, "iter_speci": 7, "itertool": 11, "its": [0, 5, 6, 7, 9, 10, 11, 15, 16, 17, 19, 20], "itself": [11, 19], "j": [4, 7, 11, 18, 19], "jaim": 0, "jhcepa": [0, 11], "join": 15, "join_branch": [3, 5], "json": 9, "json_error": 9, "jupyt": 16, "just": [5, 11, 15, 18, 19], "k": [11, 18, 19], "kalinka": 15, "karg": [9, 20], "keep": [9, 10, 11, 15, 16, 19, 20], "keep_serv": [9, 11, 16], "kegg": 9, "kegg_enzym": 9, "kegg_modul": 9, "kegg_numb": 9, "kegg_pathwai": 9, "kei": [5, 7, 17, 19], "kept": [10, 11, 16, 17, 19, 20], "key_text": 9, "keyword": 12, "khaki": [16, 20], "kind": [9, 18, 19], "know": 18, "known": 20, "kwarg": [7, 8, 9], "l": [7, 15, 19, 20], "lab": 0, "label": [1, 7, 9, 15, 16, 17, 19, 20], "labl": 15, "ladder": [3, 5, 11], "laef": 20, "lai": 11, "lambda": [4, 11, 15, 17, 19], "larg": [9, 11, 16, 19], "larger": 19, "last": [5, 9, 11, 19], "later": [19, 20], "latest": [10, 17], "latter": 19, "launch": 11, "layout": [1, 11, 14, 15], "layout1": 9, "layout_alnface_compact": 16, "layout_alnface_grai": 16, "layout_barplot": 16, "layout_domain": 16, "layout_fn": [1, 20], "layout_heatmap": 16, "layout_seqfac": 16, "layout_tree_styl": 16, "layoutalign": 9, "layoutautonam": 9, "layoutbarplot": 9, "layoutbestnam": 9, "layoutbigg": 9, "layoutbranchlength": 9, "layoutbranchsupport": 9, "layoutcard": 9, "layoutcazi": 9, "layoutcuratednam": 9, "layoutetediffdist": 9, "layouteukog": 9, "layoutevolev": 9, "layoutgenomiccontext": 9, "layouthumanog": 9, "layoutkeggenzym": 9, "layoutkeggmodul": 9, "layoutkeggnumb": 9, "layoutkeggpathwai": 9, "layoutlastcommonancestor": 9, "layoutleafnam": 9, "layoutnumberleav": 9, "layoutoutlin": 9, "layoutpdb": 9, "layoutpfamdomain": 9, "layoutpreferrednam": 9, "layoutproteinnam": 9, "layoutscientificnam": 9, "layoutscinam": 9, "layoutse": 9, "layoutsmartdomain": 9, "layoutucsc": 9, "layoutucsctran": 9, "lca_fac": 16, "lead": 15, "leaf": [4, 5, 6, 7, 9, 10, 11, 15, 17, 18, 19], "leaf_nam": [11, 20], "leaf_profil": 4, "leaf_styl": 16, "leafnam": 7, "least": [16, 18], "leav": [1, 4, 5, 7, 9, 11, 15, 16, 17, 18, 20], "leaves_extra": 11, "leaves_onli": 11, "left": [9, 16, 19], "legend": 9, "legendfac": 9, "legibl": 18, "len": [18, 19, 20], "lenght": [5, 11, 19], "length": [1, 6, 9, 11, 15, 19], "less": [14, 19], "let": [15, 16, 18, 19, 20], "lett": 15, "letter": [5, 7, 11, 15], "level": [1, 5, 10, 11, 15, 16, 19], "levelord": [11, 12, 19], "lgqvpeidvpsylpdlpgiandlmyiadlgpgiapsapgtipelptfhtevaeplkvgelgsgmgagpgtp": [16, 20], "librari": 1, "licens": 16, "lightgrai": 9, "lightgreen": 20, "lightsteelblu": [16, 20], "like": [9, 11, 16, 17, 18, 19], "likelihood": 0, "limit": [6, 9, 15, 18, 19, 20], "linag": [7, 17], "line": [9, 11, 16, 19, 20], "line_typ": 9, "line_width": [9, 16], "lineag": [5, 7, 10, 11, 15, 17], "linear": 16, "link": [2, 4, 7, 14, 16, 19, 20], "link_to_align": [7, 15], "link_to_arrayt": 4, "linkag": 4, "linux": 0, "list": [0, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 20], "listen": [11, 16], "littl": 0, "load": [6, 9, 11, 15, 17, 19, 20], "load_tre": 9, "load_tree_from_newick": 9, "local": [7, 10, 14, 16, 18], "localhost": [9, 11, 16], "locat": [10, 19, 20], "long": [6, 16, 19, 20], "long_branch_nod": 19, "longer": [11, 20], "longest": 19, "longnamefac": 20, "look": [5, 18, 19], "lookup": 14, "loop": 19, "lose": 19, "loss": [7, 15], "lost": [5, 19], "lower": [16, 19], "lstrip": 16, "ltnvsh": 15, "ltnvshniavqylsefgdln": 15, "ltnvshqfma": 15, "luminos": 20, "lupu": 20, "m": 19, "m1_t1": 1, "m2_t1": 1, "m2_t2": 1, "m2_t3": 1, "m_1_t2": 1, "macaca": 15, "made": [16, 20], "madrid": 0, "maeapd": 15, "maeapdetiq": 15, "maeapdetiqqfm": 15, "maeapdetiqqfmaltnvshniavqylsefg": 15, "maeapdetiqqfmaltnvshniavqylsefgdln": 15, "maeipdatiq": 15, "maeipdatiqqfmaltnvshniavqi": 15, "maeipdetiq": 15, "maeipdetiqqfmalt": 15, "mai": [15, 19], "main": [1, 2, 3, 9, 16, 17, 18, 19, 20], "maintain": [0, 20], "mainten": 9, "major": 16, "make": [1, 5, 11, 16, 17, 18, 19, 20], "make_box": 9, "make_fac": 9, "make_nam": [3, 5, 9], "make_pars": 6, "maltnvshqfmaltnvsh": 15, "mammal": [15, 20], "mammalia": 17, "mani": [1, 7, 9, 11, 15, 19, 20], "manipul": [1, 16, 19, 20], "manual": 20, "map": [7, 11, 15, 16], "map_attribut": 11, "map_featur": 15, "map_prop": 11, "map_properti": 7, "marcet": [7, 15], "margin": 20, "margin_bottom": 20, "margin_left": 20, "margin_right": 20, "margin_top": 20, "mark": 9, "master": [19, 20], "master_li": 20, "masteritem": 20, "match": [3, 4, 7, 9, 10, 11, 12, 15, 18], "matcher": [2, 3, 14], "matches2": 19, "math": [4, 16], "matplotlib": 16, "matrix": 11, "max": [16, 20], "max_fsiz": [9, 16], "max_len": 6, "max_mb": 9, "max_rf": 19, "max_siz": 9, "max_tim": 9, "max_treeko_splits_to_be_artifact": 11, "maxcolor": 16, "maximum": [0, 8, 9, 19], "maxval": 16, "mean": [4, 15, 16, 20], "mechan": 11, "melanogast": [15, 20], "member": 20, "memori": [9, 10, 19], "mention": 19, "mesothorax": 20, "metagenom": 0, "metathorax": 20, "metazoa": [15, 17, 19], "method": [0, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "metric": 19, "microbi": 0, "middl": 5, "midpoint": [3, 5, 14], "millimet": [11, 20], "min": 10, "min_fsiz": [9, 16], "min_siz": [9, 16], "min_support_ref": 11, "min_support_sourc": 11, "min_support_t1": 11, "min_support_t2": 11, "min_x": 9, "mincolor": 16, "minim": [9, 10], "minimap": 16, "minimum": 11, "minimum_dr": 9, "minimum_dx": 9, "minnow": 20, "minval": 16, "miss": [15, 19], "mistak": 19, "mix": 16, "mixed_motif": [16, 20], "mm": [11, 15, 20], "mms_001": 15, "mmu": 15, "mmu_001": 15, "mmu_002": 15, "mmu_004": 15, "moccasin": [16, 20], "mode": [1, 20], "model": [5, 11], "modfii": 16, "modif": [5, 11, 20], "modifi": [1, 14, 16, 20], "modify_face_posit": 16, "modify_face_properti": 16, "modify_node_styl": 16, "modify_tree_styl": 16, "modtifi": 16, "modul": [2, 8, 9, 12, 16, 17, 18, 19, 20], "mol": 0, "molbev": 0, "molecular": [15, 16, 20], "moment": [19, 20], "monophylet": [10, 11, 19], "monophyli": [11, 14], "more": [1, 5, 7, 11, 15, 16, 18, 19, 20], "moreov": 19, "most": [15, 16, 17, 18, 19], "motif": [9, 16, 20], "mous": [15, 16, 20], "mousea": 15, "mousec": 15, "mousefac": 20, "move": [3, 5], "mpl": 16, "msa": [15, 16], "msa_layout": 16, "msdlfnklvmrrkgisgkgpgagdgpggafa": [16, 20], "msw046": 0, "mu": [15, 17, 20], "much": 15, "mulata": 15, "multifurc": [11, 14], "multilin": 20, "multipl": [2, 3, 7, 14, 17], "mundo": [16, 20], "musculu": [15, 17, 20], "must": [16, 19, 20], "my": [4, 11, 16, 20], "my_dist_fn": 4, "my_layout": 1, "my_tre": 1, "mylayout": 20, "mylegend": 16, "mynewick": 15, "mytre": [1, 20], "mytreefil": 1, "mytreelayout": 16, "n": [6, 8, 9, 11, 15, 16, 18, 19, 20], "n1": [5, 16, 19, 20], "n2": [5, 16, 19, 20], "n2content": 10, "n2leav": 18, "n3": [16, 20], "n4": [16, 20], "n_col": 9, "n_row": 9, "name": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 17, 18, 19], "name2seq": 16, "name2taxid": 17, "name_fac": 1, "name_newick": 9, "named_lineag": [7, 10, 17], "namedtupl": 9, "namefac": 20, "names_librari": 19, "namespac": 17, "natur": [0, 19], "navig": 19, "ncbi": [7, 10, 14], "ncbi_compar": 7, "ncbi_taxonomi": 17, "ncbitaxa": [3, 17], "nchildren": 18, "ndup": 15, "neanderthalensi": 17, "necessari": [5, 11, 15, 17, 19], "need": [1, 6, 9, 10, 12, 15, 16, 19, 20], "neg": 18, "nematod": 19, "nest": 19, "never": 19, "nevertheless": 19, "new": [5, 7, 9, 11, 15, 16, 18, 19], "new_tre": 19, "newick": [3, 4, 7, 9, 11, 12, 14, 15, 16, 17, 18], "newick_onli": [7, 15], "newickerror": 6, "newli": [5, 11], "next": [9, 11, 19, 20], "nexu": 3, "nexuserror": 6, "nhx": [6, 15, 19], "niavqi": 15, "niavqylsef": 15, "nice_html": 9, "nick": 17, "node": [4, 5, 6, 7, 9, 10, 11, 12, 14, 17], "node1": [5, 11, 19], "node2": [5, 11, 19], "node2label": 19, "node2leav": 19, "node3": 19, "node_background": [16, 20], "node_id": [5, 9, 11], "node_nam": 7, "node_name_str": 15, "node_s": 9, "node_styl": [11, 20], "node_style_default": 9, "nodecolor": 9, "nodecount": 16, "nodenam": 7, "nodes": 9, "nodes_text": 6, "nodestyl": [3, 16, 20], "nodestyle_differ": 16, "nodestyle_triangl": 16, "nodetyp": 19, "non": 15, "non_conserved_color": 9, "none": [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "nopen": 20, "nor": 19, "norm_rf": 19, "normal": [9, 15, 17, 18, 19, 20], "notabl": 16, "notat": 19, "note": [1, 7, 11, 15, 16, 17, 18, 19, 20], "notebook": 16, "notic": 15, "noutahi": 0, "nov": 16, "novel": 16, "now": [15, 16, 18, 19, 20], "np": 16, "npanel": 9, "nsearch": 18, "nside": 9, "nst1": [16, 20], "nst2": [16, 20], "nst3": [16, 20], "nst4": [16, 20], "nstyle": 20, "ntree": 15, "number": [4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "numer": [16, 17], "numpi": [4, 16], "nw": [1, 4, 9, 11, 15, 16, 19, 20], "o": [11, 16, 19, 20], "o__korarchaeal": 17, "o__peptococcal": 17, "obj": 6, "object": [4, 6, 7, 9, 11, 19, 20], "obligatori": 16, "observ": 15, "obtain": [15, 19], "obvious": 19, "occupi": 16, "occur": 11, "occurr": 19, "ocur": 7, "offer": 17, "offici": 17, "often": [15, 18, 19], "og": 9, "ok": 19, "okai": 18, "old": [5, 11], "older": 15, "oldest": [7, 15], "on_first_visit": 9, "on_last_visit": 9, "onc": [15, 16, 17, 19, 20], "one": [1, 4, 7, 9, 11, 15, 16, 17, 18, 19, 20], "ones": 18, "onli": [1, 5, 7, 9, 11, 14, 15, 16, 17, 19, 20], "opac": [9, 16, 20], "open": [1, 4, 9, 10, 11, 16, 19], "open_brows": [9, 11], "open_browser_window": 9, "oper": [2, 3, 8, 11, 14, 20], "opisthokonta": 17, "opposit": 19, "optim": 11, "option": [1, 7, 12, 16, 18, 19, 20], "orang": [16, 20], "orangutan": 15, "order": [5, 11, 15, 16, 17, 19, 20], "ordercarnivora": 20, "orderless": 11, "org": [1, 11, 19], "organ": 17, "orient": 9, "origin": [0, 5, 7, 11, 15, 16, 17, 19, 20], "orphan": 19, "ortholog": 15, "orthologi": [0, 15], "other": [1, 5, 7, 11, 12, 15, 16, 17, 19, 20], "otherwis": [5, 10, 11, 15, 16], "our": [11, 15, 16, 18, 19, 20], "out_seq": [7, 15], "outfil": [7, 8, 11, 19], "outgroup": [5, 11, 14], "outlin": 9, "outline_color": 16, "outline_line_color": 16, "outline_line_width": 16, "outline_opac": 16, "outlinedfac": 16, "outlinefac": 9, "outparalog": 15, "output": [7, 8, 11, 15, 16, 18], "outsid": 14, "over": [1, 7, 8, 11, 15, 18, 19, 20], "overlap": [7, 16, 19], "overrid": 11, "overriden": 9, "overview": 14, "overwrit": 19, "overwriten": 15, "own": [1, 15, 16, 19, 20], "p": [4, 15, 16, 18, 19], "p1": 9, "p2": 9, "p__firmicutes_b": 17, "p__huberarchaeota": 17, "p__thermoproteota": 17, "packag": [1, 15, 17], "pad": [9, 11, 16], "padding_i": [9, 16], "padding_x": [9, 16], "page": [2, 15, 16, 20], "pair": [11, 15, 16, 20], "pan": [0, 15, 17, 20], "panel": 9, "para": 19, "paralog": 15, "paralogi": 15, "param": 7, "paramet": [4, 5, 7, 8, 9, 10, 11, 12, 16, 20], "paraphylet": 19, "parent": [5, 9, 10, 11, 16, 18, 19], "parent_child_t": 11, "parent_of": 9, "parenthes": 19, "parenthesi": 18, "pars": [0, 4, 7, 10, 11, 15, 17, 19], "parse_sp_nam": 7, "parser": [1, 2, 3, 4, 7, 9, 11, 12, 15, 18, 19], "part": [9, 15, 17, 18, 19, 20], "parti": 17, "partial": 19, "partit": [5, 7, 11, 15, 19], "parts_t1": 19, "parts_t2": 19, "pass": [11, 15, 16, 17, 18, 19, 20], "past": [11, 19], "path": [8, 11, 15, 19, 20], "pathogen": 0, "pathwai": 9, "pattern": [9, 12, 18, 19], "pda": [5, 11], "pdb": 9, "pdf": [11, 16, 20], "peer": 0, "per": [11, 15, 20], "perfect": 15, "perform": [9, 15, 16, 19, 20], "perman": 11, "permit": [16, 20], "permut": [11, 18], "pf": 16, "pfam": 9, "php": 11, "phy003i7zj_chick": 16, "phylemon": 0, "phylet": 19, "phylip": [7, 8], "phylip_relax": 8, "phylo": 15, "phylogenet": [0, 1, 2, 3, 5, 11, 14, 19], "phylogeni": [0, 15], "phylogenom": 0, "phylogent": 7, "phylom": 7, "phylomedb": 0, "phylosoft": 19, "phylostratigraf": 7, "phylotre": [3, 10, 15, 17, 18, 19], "phylum": 17, "pi": 9, "pickl": [9, 19], "pictur": 20, "piec": [9, 16, 20], "piechartfac": 9, "piexl": 16, "pile": [16, 20], "pink": [16, 20], "pixel": [9, 11, 16, 20], "place": [5, 11, 12, 15, 19, 20], "plai": 20, "plain": 19, "pleas": 11, "plot": [0, 20], "pname": 9, "png": [11, 20], "po": [6, 9], "point": [5, 9, 11, 15, 17, 19], "pointer": [7, 19, 20], "pointinghandcursor": 20, "polar": 19, "poli": 19, "polynod": 19, "polyphoni": 0, "polyphylet": 19, "polytomi": [5, 11, 19], "polytomy_size_limit": 11, "pop_child": 11, "popul": [1, 3, 5, 11, 16, 19, 20], "populate_uniform": [3, 5], "populate_yul": [3, 5], "popup": [9, 11], "port": [9, 11], "port_max": 9, "port_min": 9, "portal": 17, "portion": 19, "posibl": 11, "posit": [1, 5, 6, 11, 18, 19], "possess": 20, "possibl": [7, 9, 11, 15, 19, 20], "post": [1, 5, 9, 11, 19], "postord": [11, 19], "poswidth": [9, 16], "power": [16, 18], "pr_name": 11, "pr_valu": 11, "practic": 19, "pre": [1, 5, 10, 11, 16, 19, 20], "precis": 15, "precomput": 19, "predefin": [15, 20], "predict": 15, "prefer": [1, 9, 15], "prefix": 16, "preorder": [11, 19], "preprar": 17, "present": [0, 1, 7, 9, 10, 11, 15, 19], "preserve_branch_length": [11, 19], "prevent_nondicotom": 11, "previou": [15, 16, 18, 19], "previous": [9, 15, 19, 20], "primat": [15, 17, 19, 20], "print": [1, 5, 8, 11, 15, 16, 17, 18, 19], "print_frequnc": 16, "prior": 19, "probabl": 20, "process": [7, 9, 15, 17, 19], "processable_nod": 19, "produc": [0, 5, 11, 18, 19], "product": 0, "profil": [4, 20], "profilefac": 20, "program": [1, 16, 18, 19, 20], "programm": [15, 16, 20], "programmat": 0, "prop": [1, 5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "prop_nam": [11, 19], "prop_repr": 6, "prop_t1": 11, "prop_t2": 11, "proper": 19, "properti": [1, 4, 5, 6, 7, 9, 10, 11, 14, 15, 17], "proport": 20, "prot_nam": 9, "prota": 17, "protb": 17, "protc": 17, "protd": 17, "protein": [0, 9], "protocol": 11, "provid": [1, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "proxi": 15, "prun": 5, "prune": [7, 9, 10, 11, 14, 15, 16, 17], "prune_by_select": 9, "ptr": [15, 20], "ptr_001": 15, "ptr_002": 15, "ptr_004": 15, "pure": 16, "purpl": [16, 19, 20], "purpos": 15, "put": [5, 9, 11, 16], "px": [11, 20], "px0": 11, "py": [11, 16, 20], "pyqt6": 20, "python": [0, 1, 11, 12, 15, 16, 18, 19, 20], "pyx": [4, 11], "q": 19, "qaggigkaklrsmkerklekqqqkeqeqvratsqgghl": [16, 20], "qbrush": 20, "qcolor": 20, "qfmalt": 15, "qfmaltnvsh": 15, "qgraphicsellipseitem": 20, "qgraphicsitem": 20, "qgraphicsrectitem": 20, "qgraphicssimpletextitem": 20, "qpen": 20, "qt": [2, 3, 14], "qtcore": 20, "qtgui": 20, "qtwidget": 20, "queri": [7, 16, 17, 19], "question": 2, "quickli": [1, 18, 19], "quiet": [9, 11, 16], "quit": [16, 18, 20], "quot": [6, 16, 18], "r": [0, 6, 9, 15, 16, 19], "r1": 19, "r109": 7, "r2": 19, "r3": 19, "r4": 19, "r5": 19, "r6": 19, "radiu": [9, 20], "rais": [5, 11, 19], "randint": [16, 20], "random": [5, 11, 16, 19, 20], "random_branch": [1, 16, 20], "random_color": 20, "randomli": [5, 7, 11], "rang": [9, 15, 16, 20], "rank": [7, 10, 17], "rank_limit": 10, "raster": 20, "rat": 15, "ratc": 15, "rate": 15, "rather": [11, 15, 17], "ratio": [16, 20], "re": [12, 18, 19, 20], "reach": 19, "read": [2, 6, 7, 9, 14, 15, 16, 20], "read_cont": 6, "read_nod": 6, "readi": 20, "real": [5, 11, 15, 20], "realat": 18, "realiti": 11, "realli": 19, "reason": [7, 11, 15, 18, 19], "receiv": [7, 11, 20], "recogn": 17, "recommend": [11, 19], "recomput": 11, "recon_tre": 15, "reconcil": [7, 15], "reconcili": 7, "reconstruct": 0, "recov": 15, "rect": [9, 20], "rect_fac": 16, "rect_typ": 9, "rect_width": 9, "rectangl": [9, 16], "rectangular": [9, 16, 20], "rectfac": [9, 16], "recurs": 19, "recycl": [16, 20], "red": [9, 16, 20], "reeah": 15, "reeahq": 15, "ref": [16, 20], "ref_edg": 19, "ref_edges_in_sourc": 19, "ref_tre": 11, "ref_tree_attr": 11, "refer": [2, 5, 7, 11, 15, 16, 17, 19, 20], "referenc": 9, "regard": [16, 19, 20], "regex": [16, 18], "regexp": 16, "region": 9, "regular": 18, "rehang": [3, 5], "rel": [7, 11, 14, 18], "relat": [2, 5, 11, 17, 18, 19], "relationship": [11, 15, 19], "relative_dist": 15, "relax": 8, "releas": 17, "reliabl": 19, "reload": 15, "remain": 19, "rememb": 17, "remov": [1, 3, 5, 9, 11], "remove_act": 9, "remove_active_clad": 9, "remove_child": [11, 19], "remove_children": 11, "remove_search": 9, "remove_select": 9, "remove_sist": 11, "removed_nod": 19, "render": [1, 3, 11, 14, 15, 16], "replic": 20, "report": [10, 17], "repr_short": 6, "repres": [4, 5, 6, 9, 10, 11, 15, 16, 17, 19, 20], "represent": [6, 7, 8, 9, 11, 16, 19, 20], "reproduc": [0, 11, 20], "reprophylo": 0, "req_json": 9, "request": [9, 11], "requir": [7, 10, 11, 15, 17, 18, 19, 20], "rerio": 20, "reset": 9, "resolut": [11, 20], "resolv": [5, 11], "resolve_polytomi": [3, 5, 11, 19], "resourc": [2, 17], "respect": [5, 19], "rest": [9, 19, 20], "restrict": 12, "result": [4, 5, 8, 9, 10, 11, 15, 18, 19], "retain": 11, "retriev": [9, 15, 17, 19], "retrieve_layout": 9, "retrieve_tree_data": 9, "return": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19, 20], "return_copi": 7, "return_tre": [10, 17], "revers": [5, 9, 11], "reverse_children": 11, "review": 19, "rf": [11, 19], "rf_max": [11, 19], "rgb": 20, "rgradient": [16, 20], "rhombu": 9, "rhombus_typ": 9, "rid": 10, "right": [1, 9, 11, 16, 19, 20], "rise": 15, "rmsd": 0, "robinson": 11, "robinson_fould": [11, 19], "rodent": 20, "rokubacterial": 16, "root": [5, 7, 11, 14, 16, 17, 18, 20], "root_at": [3, 5], "root_opening_factor": 20, "root_styl": 16, "rooted_tre": 19, "rotat": [9, 16], "rotate_text": 16, "rousseeuw": 4, "row": [4, 9, 11], "royalblu": 20, "rreeahqfma": 15, "rs_gcf_000019605": 17, "rs_gcf_003948265": 17, "rstrip": 16, "rule": [16, 20], "run": [1, 16, 18], "run_smartview": 9, "rvsdsipplpppqqpqaed": [16, 20], "rx": 9, "ry": 9, "s1": 9, "s2": 9, "s__b65": 17, "s__jacael01": 17, "s__korarchaeum": 17, "s__mp8t": 17, "s__owc5": 17, "s__shmx01": 17, "s__smtz1": 17, "s__tekir": 17, "s__wtck01": 17, "safe": [9, 19], "safe_mod": 9, "safe_str": 9, "safer": [9, 12], "safer_ev": [3, 9, 12], "sai": 19, "same": [1, 7, 9, 11, 15, 16, 17, 18, 19, 20], "sametre": 15, "sampl": 17, "sample1": 16, "san": [9, 16], "sapien": [15, 17, 20], "sarcopterygii": 17, "satisfi": [12, 16], "satur": 20, "save": [1, 9, 15, 16, 19, 20], "scale": [7, 9, 15, 16], "scale_rang": [9, 16], "scalefac": [9, 16], "scan": [7, 15], "scheme": [16, 19], "sci_nam": [7, 9, 10, 11, 17], "scientif": [7, 9, 10, 17, 20], "scikit": 11, "scipi": 0, "score": [10, 15, 19], "scratch": 20, "script": [0, 1, 17], "se": 20, "search": [2, 3, 5, 9, 11, 12, 18], "search_ancestor": [11, 19], "search_by_s": 19, "search_descend": [11, 19], "search_leaves_by_nam": [11, 19], "search_nod": [11, 15, 19], "search_to_select": 9, "searched_bi": 9, "second": [9, 15, 18, 19], "section": [6, 16, 19], "section_nam": 6, "sector": 9, "see": [4, 7, 9, 11, 15, 16, 18, 19, 20], "seed": [9, 11], "seem": 18, "seen": [1, 7, 11, 19], "segment": 9, "select": [5, 9, 11, 19], "selected_children": 9, "selected_fac": 9, "selected_face_po": 9, "selectedcirclefac": 9, "selectedfac": 9, "selectedrectfac": 9, "self": [5, 7, 9, 11, 16, 19, 20], "semi": 20, "sensit": 16, "sent": [16, 20], "sep": 16, "separ": [15, 19], "seq": [7, 8, 16, 20], "seq1": 8, "seq2": 8, "seq_fac": 16, "seq_format": [9, 16, 20], "seq_motif_fac": 20, "seqa": 15, "seqb": 15, "seqc": 15, "seqd": 15, "seqfac": [9, 16, 20], "seqgroup": [2, 3, 15], "seqmotiffac": [9, 16, 20], "seqs_str": 8, "seqtyp": [9, 16], "sequenc": [2, 3, 5, 7, 9, 11, 14], "sequencefac": [16, 20], "sequenci": 8, "seri": [5, 9, 11], "serial": 19, "serialis": [11, 19], "serif": [9, 16], "serious": 19, "serra": 0, "serv": [11, 17], "server": [0, 3, 11, 16, 17], "session": [11, 18, 20], "set": [4, 5, 7, 8, 9, 10, 11, 14, 15, 16, 19, 20], "set_distance_funct": 4, "set_midpoint_outgroup": [3, 5], "set_node_styl": [9, 16], "set_outgroup": [3, 5, 11, 19], "set_seq": 8, "set_species_naming_funct": [7, 15], "set_styl": [11, 16, 20], "set_tree_styl": [9, 16], "setacceptshoverev": 20, "setbrush": 20, "setcursor": 20, "setparentitem": 20, "setpen": 20, "setpo": 20, "setrect": 20, "settext": 20, "setvis": 20, "setzvalu": 20, "sever": [0, 1, 11, 15, 16, 17, 18, 19, 20], "shape": [16, 20], "share": [11, 17, 19], "shell": 1, "shift": 5, "short": [5, 11, 18], "shortcut": [1, 16, 18], "should": [5, 7, 11, 12, 15, 16, 19, 20], "show": [1, 9, 11, 15, 19], "show_branch_length": [11, 16, 20], "show_branch_support": [11, 16, 20], "show_intern": [11, 15, 19], "show_leaf_nam": [1, 11, 16, 20], "shown": [9, 15, 16, 20], "sibl": 17, "side": [7, 11, 16], "signifi": 17, "signific": 19, "significantli": 15, "silhouet": 4, "silhouett": 4, "silouett": 4, "sim": 10, "simiiform": 17, "similar": [10, 12, 16, 17, 19], "similarli": [15, 19], "simpl": [1, 4, 14, 15, 17, 19, 20], "simple_motif": [16, 20], "simpler": 15, "simpli": [16, 20], "sinc": [11, 15, 17, 18, 19], "singl": [4, 7, 10, 11, 15, 16, 19, 20], "sister": [5, 11, 19], "site": 10, "size": [1, 5, 7, 9, 10, 11, 16, 19, 20], "size_prop": 9, "skbio_tre": 11, "skbiotre": 11, "skip": 17, "skip_large_polytomi": 11, "skip_quoted_nam": 6, "skip_spaces_and_com": 6, "skyblu": 16, "slice_typ": 9, "slightli": [1, 19], "slist": 15, "slowdown": 19, "slower": [11, 19], "slowest": [11, 19], "sm_style": [9, 11, 16], "small": [1, 16, 19, 20], "small_t": 20, "smaller": [16, 19], "smallest": 17, "smart": [9, 16], "smartview": [2, 3, 11, 16], "so": [1, 5, 7, 11, 16, 17, 18, 19], "socket": 9, "softwar": 19, "solid": [9, 16, 20], "solut": [11, 19], "solv": 14, "some": [9, 15, 16, 17, 19, 20], "someth": [12, 18], "sometim": [19, 20], "sort": [3, 5, 9, 10, 11, 20], "sort_descend": 11, "sos_thr": [7, 15], "sourc": [4, 6, 7, 8, 9, 10, 12, 16, 19, 20], "source_edg": 19, "source_edges_in_ref": 19, "source_subtre": 19, "source_tree_attr": 11, "sp": [16, 17], "sp001563325": 17, "sp001563335": 17, "sp001940705": 17, "sp002825465": 17, "sp002825515": 17, "sp002825535": 17, "sp002965065": 16, "sp003344655": 17, "sp003345545": 17, "sp003345555": 17, "sp003345595": 17, "sp003662765": 17, "sp004376265": 17, "sp004524435": 17, "sp004524445": 17, "sp004524565": 17, "sp004524595": 17, "sp005281345": 16, "sp008080745": 17, "sp011364905": 17, "sp011364985": 17, "sp011365025": 17, "sp013138615": 17, "sp013388835": 17, "sp020833055": 17, "sp_naming_funct": [7, 15, 17], "spain": 0, "span": 9, "sparingli": 18, "spci": 7, "spcode": [15, 17], "spearman_dist": 4, "speci": [0, 1, 7, 10, 11, 14, 16, 18, 19, 20], "special": [16, 18, 19, 20], "speciat": [7, 15, 19], "speciation_color": 9, "species2ag": [7, 15], "species_tre": 7, "species_tree_nw": 15, "specif": [7, 16, 17, 19, 20], "specifi": [1, 4, 9, 11, 15, 19], "speed": [11, 15], "sphere": 20, "split": [7, 17, 19], "split_by_dup": [7, 15], "split_thru_negative_xaxi": 9, "spname": 7, "spt": 15, "sptree": 15, "spx": 16, "sqlite": 17, "squar": [9, 16], "stack": 9, "stackedbarfac": 9, "stackoverflow": 0, "standalon": [1, 15], "standard": [7, 11, 19, 20], "start": [1, 5, 6, 9, 11, 16, 18, 19, 20], "startswith": [15, 16, 20], "state": 15, "statement": 19, "static": [11, 16, 20], "statist": 9, "statu": 9, "step": [5, 11, 17, 19], "still": [5, 11], "stolpii": 17, "store": [7, 8, 9, 11, 12, 15, 16, 17, 19], "store_act": 9, "store_search": 9, "store_select": 9, "str": [7, 9, 11], "straightforward": 16, "strain": 10, "strategi": [1, 11, 12, 17, 19], "streptomedb": 0, "streptomycet": 0, "strict": [15, 19], "strictli": [15, 19], "string": [1, 4, 7, 8, 11, 12, 15, 19], "stroke_color": 9, "stroke_width": 9, "strongli": [12, 19], "structur": [0, 2, 4, 7, 11, 14, 15, 16, 18, 20], "studi": [7, 15], "style": [1, 9, 11, 14], "style1": 20, "style2": 20, "sub": [9, 10, 18, 19], "subclass": 9, "subfamili": 17, "subformat": 1, "submodul": 9, "subpart": [15, 19], "subset": 19, "subsp": 17, "subspeci": [17, 20], "substitut": [5, 15, 18], "subtre": [7, 9, 12, 16, 18, 19, 20], "success": 19, "suit": [14, 16], "sum": [5, 11, 19], "summar": 9, "summari": 9, "summarize_inner_nod": 9, "sup": 18, "super": [16, 20], "superior": 19, "superkingdom": 17, "superord": 17, "supli": 11, "suppli": [7, 11], "support": [0, 5, 6, 8, 9, 11, 18, 19], "support_fn": [5, 11], "sure": 11, "svg": [11, 16, 20], "swap": 5, "swap_children": 11, "swap_prop": [3, 5], "symmetr": 11, "synonym": 15, "syntax": 19, "system": [10, 20], "t": [0, 1, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "t1": [1, 4, 11, 19], "t2": [1, 4, 11, 15, 19], "t3": [4, 11, 19], "t4": [4, 11], "tabl": [11, 16, 20], "tag": 19, "take": [7, 15, 17, 18, 19], "talk": 9, "tar": [10, 17], "targer": 16, "target": [11, 16, 19], "target2": 11, "task": [9, 19], "tax": 10, "tax2lineag": [7, 17], "tax2nam": [7, 10, 17], "tax2rank": [7, 10, 17], "tax2track": [7, 10, 17], "taxa": [10, 14], "taxa_lineag": 10, "taxdump": [10, 17], "taxdump_fil": 10, "taxid": [7, 9, 10, 14], "taxid2nam": 17, "taxid_attr": [7, 10, 17], "taxnam": 10, "taxon": 17, "taxonom": [14, 17], "taxonomi": [2, 3, 7, 14], "taxonomic_info": 15, "taxonomyi": 17, "techniqu": 19, "teleostomi": 17, "tell": 18, "tempor": [7, 15], "ten": 15, "tend": 16, "term": 19, "termin": [1, 11, 15, 16, 19, 20], "test": [0, 14], "tetrapoda": 17, "text": [6, 8, 9, 11, 15, 16, 17, 19, 20], "text_arrai": 4, "text_color": 9, "text_sect": 6, "text_typ": 9, "textcolor": 9, "textfac": [9, 16, 20], "th": 20, "than": [1, 5, 11, 15, 16, 17, 19, 20], "thats": 16, "thei": [6, 7, 11, 15, 16, 17, 19, 20], "them": [1, 5, 8, 10, 11, 15, 16, 18, 19, 20], "themselv": [11, 19], "therefor": [15, 16, 19], "theria": 17, "theta": 11, "thi": [1, 4, 5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "thing": [11, 18], "third": [17, 19], "those": [11, 15, 16], "thousand": 15, "three": [11, 15, 16, 18, 19], "threshold": [15, 16], "through": [15, 16, 17, 19, 20], "thu": [11, 15, 16, 19, 20], "thvmlgaeteeklfdaplsiskreqleqqvpenyfyvpd": [16, 20], "tick_width": [9, 16], "tid": 9, "time": [15, 17, 18, 19, 20], "timer": 9, "tip": [7, 9, 11, 18, 19], "tip1": 1, "titl": [9, 16], "tmp": 9, "tmsqfnfssapagggfsfstpkt": 16, "to_dendrogram": [3, 5], "to_hex": 16, "to_rgb": 16, "to_str": [11, 15, 17, 18, 19], "to_ultrametr": [1, 3, 5, 11], "togeth": [16, 19], "too": [5, 7, 11, 12, 19], "tool": [2, 19], "toolkit": [0, 17, 19, 20], "tooltip": [9, 16], "tooltip_prop": 9, "top": [9, 11, 16, 19, 20], "top_textfac": 16, "toplog": 19, "topmost": 19, "topolog": [5, 7, 11, 15, 18, 19], "topologi": [1, 5, 7, 11, 14, 15, 16, 20], "total": 19, "touch_and_get": 9, "tp": 18, "track": [7, 10, 17], "tran": 9, "transfer": [11, 19], "transform": 6, "translat": [6, 7, 10, 15, 17], "translate_to_nam": [10, 17], "transpar": [10, 16, 17, 20], "travers": [1, 3, 5, 11, 14, 18, 20], "traverse_bf": [3, 5], "tree": [0, 2, 3, 4, 6, 9, 10, 14], "tree1": 19, "tree2": 19, "tree_class": 6, "tree_data": 9, "tree_fac": 20, "tree_id": 9, "tree_layout": 16, "tree_styl": [1, 9, 11, 15, 16, 20], "tree_text": 6, "tree_width": 20, "treeactiv": 9, "treedata": 9, "treefac": 20, "treefil": 16, "treeko": [0, 7, 19], "treeko_dist": 19, "treelayout": 16, "treelayout_1": 16, "treematch": 18, "treenod": 11, "treepattern": [3, 12, 18], "treestyl": [1, 3, 11, 15, 16, 20], "treestyle_1": 16, "treestyle_legend": 16, "treeview": [2, 3, 20], "triangl": [9, 16], "triangle_node_styl": 16, "triangle_typ": 9, "trie": 0, "trig": 16, "trigger": 16, "tripl": 18, "troglodyt": [15, 17, 20], "tropic": 20, "true": [1, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 19, 20], "try": [9, 18], "try_synonym": 10, "ttttttttttttt": 8, "tupl": [8, 9, 11, 20], "tutori": [1, 2], "tutorial_tre": 1, "tw": 20, "two": [4, 5, 11, 15, 16, 18, 19, 20], "txt": 9, "type": [1, 9, 11, 15, 16, 19, 20], "typic": [5, 11], "u": [6, 16, 19, 20], "uba": 16, "uba2009": 16, "ucsc": 9, "ucsc_tran": 9, "ucsc_trans_prop": 9, "ugly_name_fac": 20, "ultrametr": [1, 5, 9, 11, 16], "unalign": 15, "unclassifi": 17, "uncommon": 19, "under": [0, 4, 10, 11, 15, 16, 19], "underscor": 15, "understand": [14, 16], "understood": [16, 19, 20], "unicod": 6, "uniform": [5, 11], "uniformli": 11, "uniqu": [7, 9, 11, 17], "unit": [0, 11, 20], "unless": 19, "unnecessari": 19, "unquot": 6, "unroot": [3, 5, 11], "unrooted_tre": [11, 19], "unselect_nod": 9, "until": 11, "up": [11, 14, 18, 19, 20], "updat": [5, 8, 9, 10, 11, 15, 17], "update_app_available_layout": 9, "update_layout": 9, "update_node_prop": 9, "update_node_styl": 9, "update_s": [3, 5], "update_select": 9, "update_sizes_al": [3, 5], "update_sizes_from": [3, 5], "update_taxonomy_databas": [10, 17], "upgrad": 16, "upper": [10, 19], "us": [2, 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 19, 20], "usag": 16, "use_collater": 11, "useless": 15, "user": [4, 11, 16, 17, 19, 20], "usual": [15, 17, 19], "util": [16, 17], "utterli": 9, "v": [0, 16, 20], "v0": 16, "v3": 16, "v4": [16, 17], "valencia": 0, "valid": [4, 5, 7, 9, 10, 11, 19], "valu": [4, 5, 7, 9, 11, 15, 16, 17, 18, 19, 20], "value_rang": [9, 16], "vari": 15, "variabl": [9, 14, 16], "variant": 18, "variat": 19, "variou": 16, "ve": 17, "vector": [1, 20], "veri": [16, 19, 20], "versa": 17, "version": [1, 7, 9, 12, 15, 17, 19], "vertebr": 15, "vertebrata": 17, "vertic": [9, 16], "verticl": 16, "vice": 17, "viceversa": 5, "view": [19, 20], "viewport": 9, "visit": [11, 19], "visual": [0, 2, 11, 14, 19], "vowel": [16, 19, 20], "vowel_color": 16, "vowel_node_layout": 16, "vowel_node_s": 16, "vowel_textfac": 16, "vowel_tree_styl": 16, "vqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "vt_line_color": [16, 20], "vt_line_typ": [16, 20], "vt_line_width": [9, 16, 20], "w": [1, 11, 16, 19, 20], "wa": [0, 5, 6, 19, 20], "wai": [0, 1, 11, 15, 17, 18, 19, 20], "walk": [3, 5], "walker": [3, 5], "want": [1, 5, 11, 16, 18, 19, 20], "we": [5, 9, 11, 15, 16, 17, 18, 19, 20], "web": [0, 2, 3, 14, 17], "weight": 20, "well": [10, 15, 19], "were": 19, "werkmanii": 16, "what": [9, 12, 16, 18, 19], "whatev": 9, "when": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "where": [5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "whether": 16, "which": [7, 11, 15, 16, 17, 19, 20], "while": [15, 17, 20], "white": [16, 20], "whitespac": 6, "whole": [11, 15, 17, 19, 20], "whose": [5, 16, 19, 20], "wide": [7, 15, 19], "width": [9, 11, 16, 20], "win": 18, "window": 9, "wing": 20, "within": [7, 9, 11, 14, 15, 16, 17], "without": [11, 15, 19], "wolf": 20, "won": 11, "word": [0, 10, 15, 19], "work": [2, 7, 14, 20], "world": 9, "would": [9, 15, 18, 19], "wrap": 16, "write": [2, 7, 8, 11, 14, 15, 16, 18], "written": [8, 20], "wsgirefserv": 16, "www": 19, "x": [4, 6, 9, 11, 16, 18], "xor": 11, "xx": 18, "y": [4, 6, 9, 11, 16, 18, 19], "yasqtddikd": 15, "yasqtddqpd": 15, "yayqtddqkd": 15, "yayqtddqkdrreeahqfmaltnvsh": 15, "ye": [1, 15, 18], "yeast": [15, 19], "yeast_1": 15, "yeast_2": 15, "yellow": [16, 19, 20], "yield": [4, 5, 9, 11, 12, 18, 19], "you": [1, 7, 8, 15, 16, 17, 19, 20], "younga": 16, "youngblut": 17, "your": [1, 15, 16, 17, 19], "yqtddqkdrreeah": 15, "yule": [5, 11], "yyasqtddikdrreeah": 15, "z": 11, "za": 16, "zebrafish": 20, "zero": [11, 19], "zoom": [9, 16], "zvalu": 20, "zx": [9, 16], "zy": [9, 16]}, "titles": ["About", "Frequently Asked Questions", "Welcome to ETE\u2019s documentation!", "Reference Guide", "Clustering", "Tree operations", "Parsers", "Phylogenetic trees", "Multiple Sequence Alignments (SeqGroup)", "Smartview (web graphics)", "Taxonomy databases", "Tree (main class)", "Tree matcher", "Treeview (qt graphics)", "Tutorial", "Phylogenetic trees", "Tree drawing and exploration (web)", "Taxonomy databases", "Tree matcher", "Working with the Tree structure", "Tree drawing (Qt)"], "titleterms": {"": [2, 16, 19], "1": 16, "180": 20, "2": 16, "3": 16, "A": [15, 18], "The": 19, "about": 0, "ad": 15, "add": [16, 20], "advanc": [16, 19], "algorithm": 15, "align": [8, 15, 16], "all": [1, 19], "ancestor": 19, "annot": [1, 16, 17, 19], "ar": 1, "ask": 1, "aspect": [16, 20], "attribut": 19, "automat": [15, 17], "background": [16, 20], "bar": 16, "basic": 19, "between": [17, 19, 20], "branch": [1, 16, 19, 20], "brows": [1, 19], "bubbl": 20, "cach": 19, "can": 1, "chang": 20, "check": 19, "circular": [1, 20], "clade": 16, "class": 11, "closer": 15, "cluster": 4, "collaps": [15, 16, 19], "color": 16, "combin": [16, 20], "common": 19, "compar": 19, "concaten": 19, "content": [1, 2, 9, 13, 15, 16, 17, 18, 19, 20], "context": 9, "control": [1, 15, 16], "copi": [17, 19], "creat": [19, 20], "criteria": 19, "custom": [15, 16, 19, 20], "databas": [10, 17], "date": 15, "default": 9, "defin": 16, "degre": 20, "delet": 19, "descend": [17, 19], "detach": 19, "detect": 15, "differ": 17, "distanc": 19, "do": 1, "document": 2, "domain": [9, 16, 20], "download": 16, "draw": [1, 9, 16, 20], "drawer": 9, "duplic": [15, 19], "eggnog6": 9, "elimin": 19, "et": [0, 1, 2, 19], "ete4": 17, "etecompar": 9, "event": 15, "evocel": 9, "evol_ev": 9, "evolev": 7, "evolutionari": 15, "exampl": [16, 18], "explor": 16, "export": 1, "express": [16, 18], "face": [9, 13, 16, 20], "famili": 15, "faster": 19, "find": [1, 19], "first": 19, "fix": [16, 20], "format": 1, "fould": 19, "frequent": 1, "from": [18, 19], "function": [16, 19, 20], "gene": 15, "gener": 1, "get": [17, 19], "given": 19, "graphic": [9, 13], "gtdb": 17, "gtdbtaxa": 10, "guid": 3, "heatmap": 16, "helper": 9, "highlight": 0, "how": [1, 19], "i": 1, "imag": [1, 20], "img": 20, "implement": 15, "improv": 1, "indic": 2, "info": 15, "inform": [15, 17], "interact": [16, 20], "intern": 1, "iter": 19, "its": 1, "layout": [9, 16, 20], "leaf": [1, 16, 20], "leav": 19, "legend": [16, 20], "length": [16, 20], "less": 18, "link": [0, 15], "list": 19, "load": 1, "local": 17, "look": 15, "lookup": 19, "main": 11, "manual": 15, "map": 20, "match": [16, 19], "matcher": [12, 18], "mean": 19, "midpoint": 19, "mode": 16, "modifi": 19, "monophyli": 19, "multifurc": 19, "multipl": [8, 15, 16], "name": [1, 16, 20], "ncbi": 17, "ncbi_taxonomi": 9, "ncbitaxa": 10, "newick": [1, 6, 19], "nexu": 6, "node": [1, 15, 16, 18, 19, 20], "nodestyl": [9, 13], "object": [15, 16], "onli": 18, "oper": [5, 19], "order": 1, "outgroup": [15, 19], "outlin": 16, "outsid": 18, "overlap": 15, "overral": 16, "overview": [15, 16, 17, 20], "panel": 16, "parser": 6, "phylocloud_egg5": 9, "phylogenet": [7, 15, 20], "phylotre": 7, "plot": 16, "pop": 16, "posit": [9, 16, 20], "possibl": 16, "properti": [16, 19, 20], "prune": 19, "qt": [13, 20], "question": 1, "read": [1, 19], "reconcili": 15, "refer": 3, "regular": 16, "rel": [15, 19], "relat": 0, "remov": 19, "render": [9, 20], "resourc": 0, "robinson": 19, "root": [15, 19], "rotat": 20, "scale": 20, "scratch": 19, "script": 16, "search": [16, 19], "select": 16, "separ": 20, "seq": 9, "seqgroup": 8, "sequenc": [8, 15, 16, 20], "server": 9, "session": 16, "set": 17, "shortcut": 19, "show": [16, 20], "simpl": [16, 18], "smartview": 9, "so": 15, "solv": 19, "speci": [15, 17], "specif": 15, "split": 15, "spongilla": 9, "standalon": 16, "stapl": 9, "strip": 16, "structur": 19, "style": [16, 20], "suit": 18, "support": [1, 16, 20], "svg": 1, "tab": 16, "tabl": 2, "taxa": 17, "taxid": 17, "taxonom": 15, "taxonomi": [10, 17], "test": 18, "titl": 20, "tool": 0, "topolog": 16, "topologi": [17, 18, 19], "travers": 19, "tree": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "treeko": 15, "treelayout": 9, "treestyl": [9, 13], "treeview": 13, "tutori": 14, "unbalanc": 1, "understand": 19, "unroot": 19, "up": [16, 17], "us": [0, 1, 17], "variabl": 18, "verbos": 16, "veri": 1, "visit": 1, "visual": [1, 15, 16, 20], "web": [9, 16], "welcom": 2, "which": 1, "while": 19, "within": [1, 19, 20], "work": [15, 19], "write": [1, 19], "x": 20, "y": 20, "your": 20, "zoom": 20}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"1) Layout Tab": [[16, "layout-tab"]], "2) Search & Selection Tab": [[16, "search-selection-tab"]], "3) Advanced Tab": [[16, "advanced-tab"]], "A closer look to the evolutionary event object": [[15, "a-closer-look-to-the-evolutionary-event-object"]], "A less simple example (with node expressions)": [[18, "a-less-simple-example-with-node-expressions"]], "A simple example (only topology)": [[18, "a-simple-example-only-topology"]], "About": [[0, "about"]], "Add legend": [[16, "add-legend"]], "Add legend and title": [[20, "add-legend-and-title"]], "Adding taxonomic information": [[15, "adding-taxonomic-information"]], "Advanced Layout functions": [[16, "advanced-layout-functions"]], "Advanced traversing": [[19, "advanced-traversing"]], "Automatic (custom) control of the species info": [[15, "automatic-custom-control-of-the-species-info"]], "Automatic control of species info": [[15, "automatic-control-of-species-info"]], "Automatic rooting (outgroup detection)": [[15, "automatic-rooting-outgroup-detection"]], "Automatic tree annotation using NCBI/GTDB taxonomy": [[17, "automatic-tree-annotation-using-ncbi-gtdb-taxonomy"]], "Bar Plot": [[16, "bar-plot"]], "Basic tree attributes": [[19, "basic-tree-attributes"]], "Browsing trees (traversing)": [[19, "browsing-trees-traversing"]], "Bubble tree maps": [[20, "bubble-tree-maps"]], "Caching tree content for faster lookup operations": [[19, "caching-tree-content-for-faster-lookup-operations"]], "Can ETE draw circular trees?": [[1, "can-ete-draw-circular-trees"]], "Can I control the order in which nodes are visited?": [[1, "can-i-control-the-order-in-which-nodes-are-visited"]], "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"]], "Change branch length scale (zoom in x)": [[20, "change-branch-length-scale-zoom-in-x"]], "Change branch separation between nodes (zoom in y)": [[20, "change-branch-separation-between-nodes-zoom-in-y"]], "Checking the monophyly of properties within a tree": [[19, "checking-the-monophyly-of-properties-within-a-tree"]], "Circular tree in 180 degrees": [[20, "circular-tree-in-180-degrees"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "Collapse species specific duplications": [[15, "collapse-species-specific-duplications"]], "Collapsing nodes while traversing": [[19, "collapsing-nodes-while-traversing"]], "Color Strip": [[16, "color-strip"]], "Combining styles, faces and layouts": [[16, "combining-styles-faces-and-layouts"], [20, "combining-styles-faces-and-layouts"]], "Comparing trees": [[19, "comparing-trees"]], "Concatenating trees": [[19, "concatenating-trees"]], "Contents": [[1, "contents"], [9, "contents"], [13, "contents"], [15, "contents"], [16, "contents"], [17, "contents"], [18, "contents"], [19, "contents"], [20, "contents"]], "Contents:": [[2, null]], "Control Panel": [[16, "control-panel"]], "Copying (duplicating) trees": [[19, "copying-duplicating-trees"]], "Creating a tree": [[19, "creating-a-tree"]], "Creating trees from scratch": [[19, "creating-trees-from-scratch"]], "Creating your custom interactive faces": [[20, "creating-your-custom-interactive-faces"]], "Custom searching functions": [[19, "custom-searching-functions"]], "Customizing the aspect of trees": [[16, "customizing-the-aspect-of-trees"], [20, "customizing-the-aspect-of-trees"]], "Customizing tree style": [[16, "customizing-tree-style"]], "Define Layout objects": [[16, "define-layout-objects"]], "Detecting evolutionary events": [[15, "detecting-evolutionary-events"]], "Differences between NCBI and GTDB taxonomies in ETE4": [[17, "differences-between-ncbi-and-gtdb-taxonomies-in-ete4"]], "Distances between trees": [[19, "distances-between-trees"]], "Domain annotation": [[16, "domain-annotation"]], "Download": [[16, "download"]], "Draw helpers": [[9, "module-ete4.smartview.renderer.draw_helpers"]], "Drawer": [[9, "module-ete4.smartview.renderer.drawer"]], "EvolEvent": [[7, "evolevent"]], "Examples from the test suite": [[18, "examples-from-the-test-suite"]], "Examples of searches and possible matches": [[16, "examples-of-searches-and-possible-matches"]], "Explore interactive visualization of trees": [[16, "explore-interactive-visualization-of-trees"]], "Expression search": [[16, "expression-search"]], "Face for collapsed clades": [[16, "face-for-collapsed-clades"]], "Face positions": [[9, "module-ete4.smartview.renderer.face_positions"]], "Face properties": [[16, "face-properties"], [20, "face-properties"]], "Faces": [[9, "module-ete4.smartview.renderer.faces"], [13, "faces"]], "Faces position": [[16, "faces-position"], [20, "faces-position"]], "Find the first common ancestor": [[19, "find-the-first-common-ancestor"]], "Finding nodes by their properties": [[19, "finding-nodes-by-their-properties"]], "Fixed node styles": [[20, "fixed-node-styles"]], "Fixed node styles, faces and tree style": [[16, "fixed-node-styles-faces-and-tree-style"]], "Frequently Asked Questions": [[1, "frequently-asked-questions"]], "GTDB taxonomy": [[17, "gtdb-taxonomy"]], "GTDBTaxa": [[10, "gtdbtaxa"]], "General": [[1, "general"]], "Getting descendant taxa": [[17, "getting-descendant-taxa"]], "Getting distances between nodes": [[19, "getting-distances-between-nodes"]], "Getting leaves, descendants and node\u2019s relatives": [[19, "getting-leaves-descendants-and-node-s-relatives"]], "Getting midpoint outgroup": [[19, "getting-midpoint-outgroup"]], "Getting species tree topology": [[17, "getting-species-tree-topology"]], "Getting taxid information": [[17, "getting-taxid-information"]], "Heatmap": [[16, "heatmap"]], "Highlighted Tools Using ETE": [[0, "highlighted-tools-using-ete"]], "How do I export tree images as SVG?": [[1, "how-do-i-export-tree-images-as-svg"]], "How do I export tree node annotations using the Newick format?": [[1, "how-do-i-export-tree-node-annotations-using-the-newick-format"]], "How do I find a leaf by its name?": [[1, "how-do-i-find-a-leaf-by-its-name"]], "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 use ETE?": [[1, "how-do-i-use-ete"]], "How do I visit all nodes within a tree?": [[1, "how-do-i-visit-all-nodes-within-a-tree"]], "How do I visualize internal node names?": [[1, "how-do-i-visualize-internal-node-names"]], "How to delete/eliminate or remove/detach nodes": [[19, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Img faces": [[20, "img-faces"]], "Implementation": [[15, "implementation"]], "Indices and tables": [[2, "indices-and-tables"]], "Interactive sessions": [[16, "interactive-sessions"]], "Interactive visualization of trees": [[20, "interactive-visualization-of-trees"]], "Iterators or lists?": [[19, "iterators-or-lists"]], "Layout functions": [[20, "layout-functions"]], "Layouts": [[9, "layouts"]], "Linking phylogenetic trees with multiple sequence alignments": [[15, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Manual control of the species info": [[15, "manual-control-of-the-species-info"]], "Modifying tree topology": [[19, "modifying-tree-topology"]], "Multiple Sequence Alignments (SeqGroup)": [[8, "module-ete4.core.seqgroup"]], "NCBI taxonomy": [[17, "ncbi-taxonomy"]], "NCBITaxa": [[10, "ncbitaxa"]], "Newick": [[6, "module-ete4.parser.newick"]], "Nexus": [[6, "module-ete4.parser.nexus"]], "Node Backgrounds": [[16, "node-backgrounds"]], "Node Panel": [[16, "node-panel"]], "Node annotation": [[19, "node-annotation"]], "Node backgrounds": [[20, "node-backgrounds"]], "Node faces": [[16, "node-faces"], [20, "node-faces"]], "Node style": [[16, "node-style"], [20, "node-style"]], "NodeStyle": [[9, "module-ete4.smartview.renderer.nodestyle"], [13, "nodestyle"]], "Outlined Collapsed Clade": [[16, "outlined-collapsed-clade"]], "Outside variables": [[18, "outside-variables"]], "Overrall": [[16, "overrall"]], "Overview": [[15, "overview"], [16, "overview"], [17, "overview"], [20, "overview"]], "Parsers": [[6, "parsers"]], "PhyloTree": [[7, "phylotree"]], "Phylogenetic trees": [[7, "phylogenetic-trees"], [15, "phylogenetic-trees"]], "Phylogenetic trees and sequence domains": [[20, "phylogenetic-trees-and-sequence-domains"]], "Pruning trees": [[19, "pruning-trees"]], "Reading and writing": [[1, "reading-and-writing"]], "Reading and writing newick trees": [[19, "reading-and-writing-newick-trees"]], "Reading newick trees": [[19, "reading-newick-trees"]], "Reference Guide": [[3, "reference-guide"]], "Regular expression search": [[16, "regular-expression-search"]], "Related Links and Resources": [[0, "related-links-and-resources"]], "Relative dating of phylogenetic nodes": [[15, "relative-dating-of-phylogenetic-nodes"]], "Renderer": [[9, "renderer"]], "Rendering trees as images": [[20, "rendering-trees-as-images"]], "Robinson-Foulds distance": [[19, "robinson-foulds-distance"]], "Rotate a tree": [[20, "rotate-a-tree"]], "Search all nodes matching a given criteria": [[19, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria": [[19, "search-nodes-matching-a-given-criteria"]], "Server": [[9, "module-ete4.smartview.gui.server"]], "Setting up local copies of the NCBI and GTDB taxonomy databases": [[17, "setting-up-local-copies-of-the-ncbi-and-gtdb-taxonomy-databases"]], "Shortcuts": [[19, "shortcuts"]], "Show leaf node names, branch length and branch support": [[16, "show-leaf-node-names-branch-length-and-branch-support"], [20, "show-leaf-node-names-branch-length-and-branch-support"]], "Showing node\u2019s properties in pop up": [[16, "showing-node-s-properties-in-pop-up"]], "Simple search": [[16, "simple-search"]], "Smartview (web graphics)": [[9, "smartview-web-graphics"]], "Solving multifurcations": [[19, "solving-multifurcations"]], "Species Overlap (SO) algorithm": [[15, "species-overlap-so-algorithm"]], "Splitting gene trees by duplication events": [[15, "splitting-gene-trees-by-duplication-events"]], "Standalone scripts": [[16, "standalone-scripts"]], "Taxonomy databases": [[10, "taxonomy-databases"], [17, "taxonomy-databases"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[19, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Topological search": [[16, "topological-search"]], "Traversing (browsing) trees": [[19, "traversing-browsing-trees"]], "Tree (main class)": [[11, "tree-main-class"]], "Tree Browsing": [[1, "tree-browsing"]], "Tree Layout": [[16, "tree-layout"]], "Tree Style": [[16, "tree-style"]], "Tree drawing (Qt)": [[20, "tree-drawing-qt"]], "Tree drawing and exploration (web)": [[16, "tree-drawing-and-exploration-web"]], "Tree matcher": [[12, "module-ete4.treematcher.treematcher"], [18, "tree-matcher"]], "Tree operations": [[5, "module-ete4.core.operations"]], "Tree reconciliation algorithm": [[15, "tree-reconciliation-algorithm"]], "Tree rooting": [[19, "tree-rooting"]], "Tree style": [[20, "tree-style"]], "Tree visualization": [[1, "tree-visualization"]], "TreeKO (splitting gene trees into species trees)": [[15, "treeko-splitting-gene-trees-into-species-trees"]], "TreeLayout": [[9, "module-ete4.smartview.renderer.treelayout"]], "TreeStyle": [[9, "module-ete4.smartview.renderer.treestyle"], [13, "treestyle"]], "Trees": [[19, "trees"]], "Trees within trees": [[20, "trees-within-trees"]], "Treeview (qt graphics)": [[13, "treeview-qt-graphics"]], "Tutorial": [[14, "tutorial"]], "Understanding ETE trees": [[19, "understanding-ete-trees"]], "Verbose mode": [[16, "verbose-mode"]], "Visualization of phylogenetic trees": [[15, "visualization-of-phylogenetic-trees"]], "Visualize Multiple Sequence Alignment and Domain": [[16, "visualize-multiple-sequence-alignment-and-domain"]], "Welcome to ETE\u2019s documentation!": [[2, "welcome-to-ete-s-documentation"]], "Working with branch distances": [[19, "working-with-branch-distances"]], "Working with duplicated gene families": [[15, "working-with-duplicated-gene-families"]], "Working with the Tree structure": [[19, "working-with-the-tree-structure"]], "Writing newick trees": [[19, "writing-newick-trees"]], "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"]]}, "docnames": ["about", "faqs", "index", "reference/index", "reference/reference_clustering", "reference/reference_operations", "reference/reference_parsers", "reference/reference_phylo", "reference/reference_seqgroup", "reference/reference_smartview", "reference/reference_taxonomy", "reference/reference_tree", "reference/reference_treematcher", "reference/reference_treeview", "tutorial/index", "tutorial/tutorial_phylogeny", "tutorial/tutorial_smartview", "tutorial/tutorial_taxonomy", "tutorial/tutorial_treematcher", "tutorial/tutorial_trees", "tutorial/tutorial_treeview"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["about.rst", "faqs.rst", "index.rst", "reference/index.rst", "reference/reference_clustering.rst", "reference/reference_operations.rst", "reference/reference_parsers.rst", "reference/reference_phylo.rst", "reference/reference_seqgroup.rst", "reference/reference_smartview.rst", "reference/reference_taxonomy.rst", "reference/reference_tree.rst", "reference/reference_treematcher.rst", "reference/reference_treeview.rst", "tutorial/index.rst", "tutorial/tutorial_phylogeny.rst", "tutorial/tutorial_smartview.rst", "tutorial/tutorial_taxonomy.rst", "tutorial/tutorial_treematcher.rst", "tutorial/tutorial_trees.rst", "tutorial/tutorial_treeview.rst"], "indexentries": {"__init__() (alignedgrid method)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid.__init__", false]], "__init__() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.__init__", false]], "__init__() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.__init__", false]], "__init__() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.__init__", false]], "__init__() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.__init__", false]], "__init__() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.__init__", false]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__", false]], "__init__() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.__init__", false]], "__init__() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.__init__", false]], "__init__() (face method)": [[9, "ete4.smartview.renderer.faces.Face.__init__", false]], "__init__() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.__init__", false]], "__init__() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.__init__", false]], "__init__() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.__init__", false]], "__init__() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.__init__", false]], "__init__() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.__init__", false]], "__init__() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.__init__", false]], "__init__() (layoutbestname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName.__init__", false]], "__init__() (layoutbigg method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg.__init__", false]], "__init__() (layoutbranchlength method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength.__init__", false]], "__init__() (layoutbranchsupport method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport.__init__", false]], "__init__() (layoutcard method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard.__init__", false]], "__init__() (layoutcazy method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy.__init__", false]], "__init__() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.__init__", false]], "__init__() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.__init__", false]], "__init__() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.__init__", false]], "__init__() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.__init__", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.__init__", false]], "__init__() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.__init__", false]], "__init__() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.__init__", false]], "__init__() (layoutkeggenzyme method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme.__init__", false]], "__init__() (layoutkeggmodule method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule.__init__", false]], "__init__() (layoutkeggnumber method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber.__init__", false]], "__init__() (layoutkeggpathway method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway.__init__", false]], "__init__() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.__init__", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.__init__", false]], "__init__() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.__init__", false]], "__init__() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.__init__", false]], "__init__() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.__init__", false]], "__init__() (layoutpdb method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb.__init__", false]], "__init__() (layoutpfamdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains.__init__", false], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains.__init__", false]], "__init__() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.__init__", false]], "__init__() (layoutproteinname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName.__init__", false]], "__init__() (layoutscientificname method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName.__init__", false]], "__init__() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.__init__", false]], "__init__() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.__init__", false]], "__init__() (layoutsmartdomains method)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains.__init__", false], [9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains.__init__", false]], "__init__() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.__init__", false]], "__init__() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.__init__", false]], "__init__() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.__init__", false]], "__init__() (ncbitaxa method)": [[10, "ete4.NCBITaxa.__init__", false]], "__init__() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.__init__", false]], "__init__() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.__init__", false]], "__init__() (phylotree method)": [[7, "ete4.PhyloTree.__init__", false]], "__init__() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.__init__", false]], "__init__() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.__init__", false]], "__init__() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.__init__", false]], "__init__() (selectedcircleface method)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace.__init__", false]], "__init__() (selectedface method)": [[9, "ete4.smartview.renderer.faces.SelectedFace.__init__", false]], "__init__() (selectedrectface method)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace.__init__", false]], "__init__() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.__init__", false]], "__init__() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.__init__", false]], "__init__() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.__init__", false]], "__init__() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.__init__", false]], "__init__() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.__init__", false]], "__init__() (tree method)": [[11, "ete4.Tree.__init__", false]], "__init__() (treedata method)": [[9, "ete4.smartview.gui.server.TreeData.__init__", false]], "__init__() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.__init__", false]], "__init__() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.__init__", false]], "__init__() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.__init__", false]], "activate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_clade", false]], "activate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.activate_node", false]], "active (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Active", false]], "active (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.active", false]], "active_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face", false]], "active_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.active_face_pos", false]], "add_branch_values() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_branch_values", false]], "add_child() (tree method)": [[11, "ete4.Tree.add_child", false]], "add_children() (tree method)": [[11, "ete4.Tree.add_children", false]], "add_face() (grid method)": [[9, "ete4.smartview.renderer.face_positions.Grid.add_face", false]], "add_face() (tree method)": [[11, "ete4.Tree.add_face", false]], "add_face_smartview() (tree method)": [[11, "ete4.Tree.add_face_smartview", false]], "add_face_treeview() (tree method)": [[11, "ete4.Tree.add_face_treeview", false]], "add_feature() (tree method)": [[11, "ete4.Tree.add_feature", false]], "add_features() (tree method)": [[11, "ete4.Tree.add_features", false]], "add_leaf_names() (in module ete4.core.operations)": [[5, "ete4.core.operations.add_leaf_names", false]], "add_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.add_legend", false]], "add_next_branch() (walker method)": [[5, "ete4.core.operations.Walker.add_next_branch", false]], "add_prop() (tree method)": [[11, "ete4.Tree.add_prop", false]], "add_props() (tree method)": [[11, "ete4.Tree.add_props", false]], "add_sister() (tree method)": [[11, "ete4.Tree.add_sister", false]], "add_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_tree", false]], "add_trees_from_request() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.add_trees_from_request", false]], "aligned_panel_footer (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_footer", false]], "aligned_panel_header (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.aligned_panel_header", false]], "alignedgrid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.AlignedGrid", false]], "alignlinkface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace", false]], "alignmentface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AlignmentFace", false]], "ancestors() (tree method)": [[11, "ete4.Tree.ancestors", false]], "annotate_gtdb_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_gtdb_taxa", false]], "annotate_ncbi_taxa() (phylotree method)": [[7, "ete4.PhyloTree.annotate_ncbi_taxa", false]], "annotate_tree() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.annotate_tree", false]], "annotate_tree() (ncbitaxa method)": [[10, "ete4.NCBITaxa.annotate_tree", false]], "apply_translations() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.apply_translations", false]], "arrowface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ArrowFace", false]], "assert_root_consistency() (in module ete4.core.operations)": [[5, "ete4.core.operations.assert_root_consistency", false]], "attrface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.AttrFace", false]], "box (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Box", false]], "build_blocks() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.build_blocks", false]], "build_regions() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.build_regions", false]], "callback() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.callback", false]], "cartesian() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.cartesian", false]], "cased_name() (in module ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.cased_name", false]], "change_selection_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.change_selection_name", false]], "check_monophyly() (tree method)": [[11, "ete4.Tree.check_monophyly", false]], "children (tree attribute)": [[11, "ete4.Tree.children", false]], "circleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.CircleFace", false]], "circumasec() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumasec", false]], "circumrect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.circumrect", false]], "clades (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.clades", false]], "clip_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.clip_angles", false]], "clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree", false]], "collapse_lineage_specific_expansions() (phylotree method)": [[7, "ete4.PhyloTree.collapse_lineage_specific_expansions", false]], "collapse_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.COLLAPSE_SIZE", false]], "collapsed_faces (tree attribute)": [[11, "ete4.Tree.collapsed_faces", false]], "common_ancestor() (in module ete4.core.operations)": [[5, "ete4.core.operations.common_ancestor", false]], "common_ancestor() (tree method)": [[11, "ete4.Tree.common_ancestor", false]], "compare() (tree method)": [[11, "ete4.Tree.compare", false]], "compute_bounding_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.compute_bounding_box", false]], "compute_bounding_box() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.compute_bounding_box", false]], "compute_bounding_box() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.compute_bounding_box", false]], "compute_bounding_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_bounding_box", false]], "compute_bounding_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.compute_bounding_box", false]], "compute_bounding_box() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.compute_bounding_box", false]], "compute_bounding_box() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.compute_bounding_box", false]], "compute_bounding_box() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.compute_bounding_box", false]], "compute_bounding_box() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.compute_bounding_box", false]], "compute_bounding_box() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.compute_bounding_box", false]], "compute_fsize() (face method)": [[9, "ete4.smartview.renderer.faces.Face.compute_fsize", false]], "compute_pie() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.compute_pie", false]], "content_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.content_repr", false]], "content_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.content_size", false]], "content_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.content_size", false]], "cophenetic_matrix() (tree method)": [[11, "ete4.Tree.cophenetic_matrix", false]], "copy() (tree method)": [[11, "ete4.Tree.copy", false]], "copy_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.copy_style", false]], "create_dichotomic_sister() (in module ete4.core.operations)": [[5, "ete4.core.operations.create_dichotomic_sister", false]], "deactivate_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_clade", false]], "deactivate_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.deactivate_node", false]], "del_feature() (tree method)": [[11, "ete4.Tree.del_feature", false]], "del_prop() (tree method)": [[11, "ete4.Tree.del_prop", false]], "del_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.del_tree", false]], "delete() (tree method)": [[11, "ete4.Tree.delete", false]], "descendants() (tree method)": [[11, "ete4.Tree.descendants", false]], "describe() (tree method)": [[11, "ete4.Tree.describe", false]], "detach() (tree method)": [[11, "ete4.Tree.detach", false]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation", false]], "dist (tree attribute)": [[11, "ete4.Tree.dist", false]], "dist() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.dist", false]], "draw() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.draw", false]], "draw() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.draw", false]], "draw() (arrowface method)": [[9, "ete4.smartview.renderer.faces.ArrowFace.draw", false]], "draw() (circleface method)": [[9, "ete4.smartview.renderer.faces.CircleFace.draw", false]], "draw() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw", false]], "draw() (htmlface method)": [[9, "ete4.smartview.renderer.faces.HTMLFace.draw", false]], "draw() (imgface method)": [[9, "ete4.smartview.renderer.faces.ImgFace.draw", false]], "draw() (legendface method)": [[9, "ete4.smartview.renderer.faces.LegendFace.draw", false]], "draw() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.draw", false]], "draw() (piechartface method)": [[9, "ete4.smartview.renderer.faces.PieChartFace.draw", false]], "draw() (rectface method)": [[9, "ete4.smartview.renderer.faces.RectFace.draw", false]], "draw() (scaleface method)": [[9, "ete4.smartview.renderer.faces.ScaleFace.draw", false]], "draw() (seqface method)": [[9, "ete4.smartview.renderer.faces.SeqFace.draw", false]], "draw() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.draw", false]], "draw() (stackedbarface method)": [[9, "ete4.smartview.renderer.faces.StackedBarFace.draw", false]], "draw() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.draw", false]], "draw_aligned_headers() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_aligned_headers", false]], "draw_arc() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arc", false]], "draw_array() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_array", false]], "draw_arrow() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_arrow", false]], "draw_childrenline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_childrenline", false]], "draw_childrenline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_childrenline", false]], "draw_circle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_circle", false]], "draw_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_collapsed", false]], "draw_collapsed() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_collapsed", false]], "draw_collapsed() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_collapsed", false]], "draw_collapsed() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_collapsed", false]], "draw_collapsed() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_collapsed", false]], "draw_content() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_content", false]], "draw_ellipse() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_ellipse", false]], "draw_html() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_html", false]], "draw_img() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_img", false]], "draw_lengthline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_lengthline", false]], "draw_lengthline() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_lengthline", false]], "draw_line() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_line", false]], "draw_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.draw_node", false]], "draw_node() (drawercircfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces.draw_node", false]], "draw_node() (drawerrectfaces method)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces.draw_node", false]], "draw_nodebox() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodebox", false]], "draw_nodebox() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodebox", false]], "draw_nodebox() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_nodebox", false]], "draw_nodedot() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.draw_nodedot", false]], "draw_nodedot() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.draw_nodedot", false]], "draw_outline() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_outline", false]], "draw_rect() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rect", false]], "draw_rhombus() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_rhombus", false]], "draw_slice() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_slice", false]], "draw_text() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_text", false]], "draw_triangle() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.draw_triangle", false]], "drawer (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Drawer", false]], "draweraligncircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces", false]], "draweralignrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces", false]], "drawercirc (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc", false]], "drawercircfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerCircFaces", false]], "drawerrect (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRect", false]], "drawerrectfaces (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.DrawerRectFaces", false]], "drawn_size() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.drawn_size", false]], "dump() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dump", false]], "dumps() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.dumps", false]], "dx (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dx", false]], "dx (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dx", false]], "dy (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.dy", false]], "dy (size attribute)": [[9, "ete4.smartview.renderer.drawer.Size.dy", false]], "edges() (tree method)": [[11, "ete4.Tree.edges", false]], "error() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.error", false]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree", false]], "ete4.core.operations": [[5, "module-ete4.core.operations", false]], "ete4.core.seqgroup": [[8, "module-ete4.core.seqgroup", false]], "ete4.parser.newick": [[6, "module-ete4.parser.newick", false]], "ete4.parser.nexus": [[6, "module-ete4.parser.nexus", false]], "ete4.smartview.gui.server": [[9, "module-ete4.smartview.gui.server", false]], "ete4.smartview.renderer.draw_helpers": [[9, "module-ete4.smartview.renderer.draw_helpers", false]], "ete4.smartview.renderer.drawer": [[9, "module-ete4.smartview.renderer.drawer", false]], "ete4.smartview.renderer.face_positions": [[9, "module-ete4.smartview.renderer.face_positions", false]], "ete4.smartview.renderer.faces": [[9, "module-ete4.smartview.renderer.faces", false]], "ete4.smartview.renderer.layouts.context_layouts": [[9, "module-ete4.smartview.renderer.layouts.context_layouts", false]], "ete4.smartview.renderer.layouts.default_layouts": [[9, "module-ete4.smartview.renderer.layouts.default_layouts", false]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, "module-ete4.smartview.renderer.layouts.domain_layouts", false]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, "module-ete4.smartview.renderer.layouts.seq_layouts", false]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, "module-ete4.smartview.renderer.layouts.staple_layouts", false]], "ete4.smartview.renderer.nodestyle": [[9, "module-ete4.smartview.renderer.nodestyle", false]], "ete4.smartview.renderer.treelayout": [[9, "module-ete4.smartview.renderer.treelayout", false]], "ete4.smartview.renderer.treestyle": [[9, "module-ete4.smartview.renderer.treestyle", false]], "ete4.treematcher.treematcher": [[12, "module-ete4.treematcher.treematcher", false]], "evolevent (class in ete4.phylo)": [[7, "ete4.phylo.EvolEvent", false]], "exclude_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.exclude_props", false]], "expand_polytomies() (tree method)": [[11, "ete4.Tree.expand_polytomies", false]], "explore() (tree method)": [[11, "ete4.Tree.explore", false]], "face (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.Face", false]], "faces (tree attribute)": [[11, "ete4.Tree.faces", false]], "farthest() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest", false]], "farthest_descendant() (in module ete4.core.operations)": [[5, "ete4.core.operations.farthest_descendant", false]], "find_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.find_node", false]], "first_value() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.first_value", false]], "first_visit (walker property)": [[5, "ete4.core.operations.Walker.first_visit", false]], "fits() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.fits", false]], "fits() (face method)": [[9, "ete4.smartview.renderer.faces.Face.fits", false]], "fits() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.fits", false]], "fits() (seqmotifface method)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace.fits", false]], "fits() (textface method)": [[9, "ete4.smartview.renderer.faces.TextFace.fits", false]], "flush_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.flush_outline", false]], "flush_outline() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.flush_outline", false]], "from_parent_child_table() (tree static method)": [[11, "ete4.Tree.from_parent_child_table", false]], "from_skbio() (tree static method)": [[11, "ete4.Tree.from_skbio", false]], "get_active_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_active_children", false]], "get_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clade", false]], "get_active_clades() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_active_clades", false]], "get_age() (phylotree method)": [[7, "ete4.PhyloTree.get_age", false]], "get_age_balanced_outgroup() (phylotree method)": [[7, "ete4.PhyloTree.get_age_balanced_outgroup", false]], "get_asec() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_asec", false]], "get_box() (alignlinkface method)": [[9, "ete4.smartview.renderer.faces.AlignLinkFace.get_box", false]], "get_box() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.get_box", false]], "get_box() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.get_box", false]], "get_box() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_box", false]], "get_box() (outlineface method)": [[9, "ete4.smartview.renderer.faces.OutlineFace.get_box", false]], "get_broken_branches() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_broken_branches", false]], "get_broken_branches() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_broken_branches", false]], "get_cached_content() (tree method)": [[11, "ete4.Tree.get_cached_content", false]], "get_children() (tree method)": [[11, "ete4.Tree.get_children", false]], "get_closest_leaf() (tree method)": [[11, "ete4.Tree.get_closest_leaf", false]], "get_collapsed_node() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_collapsed_node", false]], "get_color() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.get_color", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.get_color", false]], "get_command_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_command_search", false]], "get_commands() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_commands", false]], "get_common_names() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_common_names", false]], "get_common_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_common_names", false]], "get_content() (attrface method)": [[9, "ete4.smartview.renderer.faces.AttrFace.get_content", false]], "get_content() (face method)": [[9, "ete4.smartview.renderer.faces.Face.get_content", false]], "get_context() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_context", false]], "get_descendant_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_descendant_evol_events", false]], "get_descendant_taxa() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_descendant_taxa", false]], "get_descendant_taxa() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_descendant_taxa", false]], "get_distance() (tree method)": [[11, "ete4.Tree.get_distance", false]], "get_drawer() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_drawer", false]], "get_drawers() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_drawers", false]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn", false]], "get_empty_active() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_empty_active", false]], "get_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_entries", false]], "get_eval_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_eval_search", false]], "get_extended_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_extended_props", false]], "get_farthest_leaf() (tree method)": [[11, "ete4.Tree.get_farthest_leaf", false]], "get_farthest_node() (tree method)": [[11, "ete4.Tree.get_farthest_node", false]], "get_farthest_oldest_leaf() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_leaf", false]], "get_farthest_oldest_node() (phylotree method)": [[7, "ete4.PhyloTree.get_farthest_oldest_node", false]], "get_fuzzy_name_translation() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_fuzzy_name_translation", false]], "get_layout_evoltype() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_evoltype", false]], "get_layout_gnames() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_gnames", false]], "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", false]], "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", false]], "get_layout_sciname() (in module ete4.smartview.renderer.layouts.phylocloud_egg5_layouts)": [[9, "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts.get_layout_sciname", false]], "get_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts", false]], "get_layouts_from_getters() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_layouts_from_getters", false]], "get_legend() (treestyle method)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.get_legend", false]], "get_line_type() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_line_type", false]], "get_lineage() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage", false]], "get_lineage_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_lineage_translator", false]], "get_midpoint_outgroup() (tree method)": [[11, "ete4.Tree.get_midpoint_outgroup", false]], "get_monophyletic() (tree method)": [[11, "ete4.Tree.get_monophyletic", false]], "get_my_evol_events() (phylotree method)": [[7, "ete4.PhyloTree.get_my_evol_events", false]], "get_name_lineage() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_name_lineage", false]], "get_name_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_name_translator", false]], "get_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_newick", false]], "get_next_available_port() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_next_available_port", false]], "get_nodes_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_nodes_info", false]], "get_outline() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_outline", false]], "get_parents() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parents", false]], "get_parser() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_parser", false]], "get_popup_props() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_popup_props", false]], "get_prop() (tree method)": [[11, "ete4.Tree.get_prop", false]], "get_props() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.get_props", false]], "get_rank() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_rank", false]], "get_rank() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_rank", false]], "get_rect() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.get_rect", false]], "get_search_function() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_search_function", false]], "get_section() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_section", false]], "get_sections() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_sections", false]], "get_selected_children() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.get_selected_children", false]], "get_selection_info() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selection_info", false]], "get_selections() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_selections", false]], "get_seq() (alignmentface method)": [[9, "ete4.smartview.renderer.faces.AlignmentFace.get_seq", false]], "get_seq() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.get_seq", false]], "get_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.get_seq", false]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette", false]], "get_sisters() (tree method)": [[11, "ete4.Tree.get_sisters", false]], "get_speciation_trees() (phylotree method)": [[7, "ete4.PhyloTree.get_speciation_trees", false]], "get_species() (phylotree method)": [[7, "ete4.PhyloTree.get_species", false]], "get_stats() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_stats", false]], "get_taxid_translator() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_taxid_translator", false]], "get_tid() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_tid", false]], "get_tooltip() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.get_tooltip", false]], "get_topological_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_topological_search", false]], "get_topology() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.get_topology", false]], "get_topology() (ncbitaxa method)": [[10, "ete4.NCBITaxa.get_topology", false]], "get_topology_id() (tree method)": [[11, "ete4.Tree.get_topology_id", false]], "get_trees() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.get_trees", false]], "get_trees_from_file() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_file", false]], "get_trees_from_form() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_form", false]], "get_trees_from_nexus_or_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.get_trees_from_nexus_or_newick", false]], "get_xs() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_xs", false]], "get_ys() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.get_ys", false]], "globalstuff (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.GlobalStuff", false]], "go_back() (walker method)": [[5, "ete4.core.operations.Walker.go_back", false]], "grid (class in ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.Grid", false]], "gtdbtaxa (class in ete4)": [[10, "ete4.GTDBTaxa", false]], "has_unvisited_branches (walker property)": [[5, "ete4.core.operations.Walker.has_unvisited_branches", false]], "htmlface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.HTMLFace", false]], "id (tree attribute)": [[11, "ete4.Tree.id", false]], "img_style (tree property)": [[11, "ete4.Tree.img_style", false]], "imgface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ImgFace", false]], "in_aligned_viewport() (face method)": [[9, "ete4.smartview.renderer.faces.Face.in_aligned_viewport", false]], "in_viewport() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.in_viewport", false]], "in_viewport() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.in_viewport", false]], "include_props (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.include_props", false]], "init() (nodestyle method)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle.init", false]], "init_from_ete() (tree method)": [[11, "ete4.Tree.init_from_ete", false]], "init_from_newick() (tree method)": [[11, "ete4.Tree.init_from_newick", false]], "initialize() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize", false]], "initialize_tree_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.initialize_tree_style", false]], "initialized (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.initialized", false]], "insert_intermediate() (in module ete4.core.operations)": [[5, "ete4.core.operations.insert_intermediate", false]], "interchange_references() (in module ete4.core.operations)": [[5, "ete4.core.operations.interchange_references", false]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist", false]], "intersects_angles() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_angles", false]], "intersects_box() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_box", false]], "intersects_segment() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.intersects_segment", false]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist", false]], "is_collapsed (tree property)": [[11, "ete4.Tree.is_collapsed", false]], "is_fully_collapsed() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.is_fully_collapsed", false]], "is_initialized (tree property)": [[11, "ete4.Tree.is_initialized", false]], "is_leaf (tree attribute)": [[11, "ete4.Tree.is_leaf", false]], "is_monophyletic() (tree method)": [[11, "ete4.Tree.is_monophyletic", false]], "is_root (tree attribute)": [[11, "ete4.Tree.is_root", false]], "is_small() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.is_small", false]], "is_small() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.is_small", false]], "iter_entries() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.iter_entries", false]], "iter_prepostorder() (tree method)": [[11, "ete4.Tree.iter_prepostorder", false]], "iter_species() (phylotree method)": [[7, "ete4.PhyloTree.iter_species", false]], "join_branch() (in module ete4.core.operations)": [[5, "ete4.core.operations.join_branch", false]], "json_error() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.json_error", false]], "ladderize() (in module ete4.core.operations)": [[5, "ete4.core.operations.ladderize", false]], "ladderize() (tree method)": [[11, "ete4.Tree.ladderize", false]], "layoutalignment (class in ete4.smartview.renderer.layouts.seq_layouts)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment", false]], "layoutautoname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName", false]], "layoutbarplot (class in ete4.smartview.renderer.layouts.staple_layouts)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot", false]], "layoutbestname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName", false]], "layoutbigg (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg", false]], "layoutbranchlength (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength", false]], "layoutbranchsupport (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport", false]], "layoutcard (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard", false]], "layoutcazy (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy", false]], "layoutcuratedname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName", false]], "layoutetediffdistance (class in ete4.smartview.renderer.layouts.etecompare_layouts)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance", false]], "layouteukogs (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents", false]], "layoutevolevents (class in ete4.smartview.renderer.layouts.evol_events_layouts)": [[9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents", false]], "layoutgenomiccontext (class in ete4.smartview.renderer.layouts.context_layouts)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext", false]], "layouthumanogs (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs", false]], "layoutkeggenzyme (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme", false]], "layoutkeggmodule (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule", false]], "layoutkeggnumber (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber", false]], "layoutkeggpathway (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor", false]], "layoutlastcommonancestor (class in ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts)": [[9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor", false]], "layoutleafname (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName", false]], "layoutnumberleaves (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves", false]], "layoutoutline (class in ete4.smartview.renderer.layouts.default_layouts)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline", false]], "layoutpdb (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains", false]], "layoutpfamdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains", false]], "layoutpreferredname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName", false]], "layoutproteinname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName", false]], "layouts (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.layouts", false]], "layoutscientificname (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName", false]], "layoutsciname (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName", false]], "layoutseeds (class in ete4.smartview.renderer.layouts.spongilla_layouts)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.domain_layouts)": [[9, "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains", false]], "layoutsmartdomains (class in ete4.smartview.renderer.layouts.eggnog6_layouts)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains", false]], "layoutucsc (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC", false]], "layoutucsctrans (class in ete4.smartview.renderer.layouts.evocell_layouts)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans", false]], "leaf_names() (tree method)": [[11, "ete4.Tree.leaf_names", false]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles", false]], "leaves() (tree method)": [[11, "ete4.Tree.leaves", false]], "legendface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.LegendFace", false]], "level (tree attribute)": [[11, "ete4.Tree.level", false]], "lineage() (tree method)": [[11, "ete4.Tree.lineage", false]], "link_to_alignment() (phylotree method)": [[7, "ete4.PhyloTree.link_to_alignment", false]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable", false]], "load() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.load", false]], "load() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.load", false]], "load_tree() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree", false]], "load_tree_from_newick() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.load_tree_from_newick", false]], "loads() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.loads", false]], "loads() (in module ete4.parser.nexus)": [[6, "ete4.parser.nexus.loads", false]], "maintenance() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.maintenance", false]], "make_box() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.make_box", false]], "make_faces() (in module ete4.smartview.renderer.face_positions)": [[9, "ete4.smartview.renderer.face_positions.make_faces", false]], "make_name() (in module ete4.core.operations)": [[5, "ete4.core.operations.make_name", false]], "make_name() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.make_name", false]], "make_parser() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.make_parser", false]], "match() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.match", false]], "match() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.match", false]], "midpoint() (in module ete4.core.operations)": [[5, "ete4.core.operations.midpoint", false]], "min_size (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.MIN_SIZE", false]], "module": [[4, "module-ete4.clustering.clustertree", false], [5, "module-ete4.core.operations", false], [6, "module-ete4.parser.newick", false], [6, "module-ete4.parser.nexus", false], [8, "module-ete4.core.seqgroup", false], [9, "module-ete4.smartview.gui.server", false], [9, "module-ete4.smartview.renderer.draw_helpers", false], [9, "module-ete4.smartview.renderer.drawer", false], [9, "module-ete4.smartview.renderer.face_positions", false], [9, "module-ete4.smartview.renderer.faces", false], [9, "module-ete4.smartview.renderer.layouts.context_layouts", false], [9, "module-ete4.smartview.renderer.layouts.default_layouts", false], [9, "module-ete4.smartview.renderer.layouts.domain_layouts", false], [9, "module-ete4.smartview.renderer.layouts.eggnog6_layouts", false], [9, "module-ete4.smartview.renderer.layouts.etecompare_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evocell_layouts", false], [9, "module-ete4.smartview.renderer.layouts.evol_events_layouts", false], [9, "module-ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts", false], [9, "module-ete4.smartview.renderer.layouts.phylocloud_egg5_layouts", false], [9, "module-ete4.smartview.renderer.layouts.seq_layouts", false], [9, "module-ete4.smartview.renderer.layouts.spongilla_layouts", false], [9, "module-ete4.smartview.renderer.layouts.staple_layouts", false], [9, "module-ete4.smartview.renderer.nodestyle", false], [9, "module-ete4.smartview.renderer.treelayout", false], [9, "module-ete4.smartview.renderer.treestyle", false], [12, "module-ete4.treematcher.treematcher", false], [13, "module-treeview", false]], "move() (in module ete4.core.operations)": [[5, "ete4.core.operations.move", false]], "name (tree attribute)": [[11, "ete4.Tree.name", false]], "name (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.name", false]], "ncbi_compare() (phylotree method)": [[7, "ete4.PhyloTree.ncbi_compare", false]], "ncbitaxa (class in ete4)": [[10, "ete4.NCBITaxa", false]], "newickerror": [[6, "ete4.parser.newick.NewickError", false]], "nexuserror": [[6, "ete4.parser.nexus.NexusError", false]], "nice_html() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.nice_html", false]], "node (walker property)": [[5, "ete4.core.operations.Walker.node", false]], "node_id (walker property)": [[5, "ete4.core.operations.Walker.node_id", false]], "node_size() (drawercirc method)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.node_size", false]], "node_size() (drawerrect method)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.node_size", false]], "nodes (treeactive attribute)": [[9, "ete4.smartview.renderer.drawer.TreeActive.nodes", false]], "nodestyle (class in ete4.smartview.renderer.nodestyle)": [[9, "ete4.smartview.renderer.nodestyle.NodeStyle", false]], "nodestyles (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.nodestyles", false]], "npanels (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.NPANELS", false]], "npanels (draweraligncircfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignCircFaces.NPANELS", false]], "npanels (draweralignrectfaces attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerAlignRectFaces.NPANELS", false]], "on_first_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_first_visit", false]], "on_last_visit() (drawer method)": [[9, "ete4.smartview.renderer.drawer.Drawer.on_last_visit", false]], "open_browser_window() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.open_browser_window", false]], "orientation (arrowface property)": [[9, "ete4.smartview.renderer.faces.ArrowFace.orientation", false]], "outlineface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.OutlineFace", false]], "padding (class in ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.Padding", false]], "parents (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.parents", false]], "phylotree (class in ete4)": [[7, "ete4.PhyloTree", false]], "piechartface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.PieChartFace", false]], "pop_child() (tree method)": [[11, "ete4.Tree.pop_child", false]], "populate() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate", false]], "populate() (tree method)": [[11, "ete4.Tree.populate", false]], "populate_uniform() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_uniform", false]], "populate_yule() (in module ete4.core.operations)": [[5, "ete4.core.operations.populate_yule", false]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile", false]], "prop_repr() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.prop_repr", false]], "props (tree attribute)": [[11, "ete4.Tree.props", false]], "prune() (tree method)": [[11, "ete4.Tree.prune", false]], "prune_by_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.prune_by_selection", false]], "quote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.quote", false]], "read_content() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_content", false]], "read_nodes() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.read_nodes", false]], "reconcile() (phylotree method)": [[7, "ete4.PhyloTree.reconcile", false]], "rectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.RectFace", false]], "rehang() (in module ete4.core.operations)": [[5, "ete4.core.operations.rehang", false]], "remove() (in module ete4.core.operations)": [[5, "ete4.core.operations.remove", false]], "remove_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active", false]], "remove_active_clade() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_active_clade", false]], "remove_child() (tree method)": [[11, "ete4.Tree.remove_child", false]], "remove_children() (tree method)": [[11, "ete4.Tree.remove_children", false]], "remove_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_search", false]], "remove_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.remove_selection", false]], "remove_sister() (tree method)": [[11, "ete4.Tree.remove_sister", false]], "render() (tree method)": [[11, "ete4.Tree.render", false]], "repr_short() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.repr_short", false]], "req_json() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.req_json", false]], "resolve_polytomy() (in module ete4.core.operations)": [[5, "ete4.core.operations.resolve_polytomy", false]], "resolve_polytomy() (tree method)": [[11, "ete4.Tree.resolve_polytomy", false]], "results (active attribute)": [[9, "ete4.smartview.renderer.drawer.Active.results", false]], "retrieve_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_layouts", false]], "retrieve_tree_data() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.retrieve_tree_data", false]], "reverse_children() (tree method)": [[11, "ete4.Tree.reverse_children", false]], "robinson_foulds() (tree method)": [[11, "ete4.Tree.robinson_foulds", false]], "root (tree attribute)": [[11, "ete4.Tree.root", false]], "root_at() (in module ete4.core.operations)": [[5, "ete4.core.operations.root_at", false]], "run_smartview() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.run_smartview", false]], "safe_string() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.safe_string", false]], "safer_eval() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.safer_eval", false]], "safer_eval() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.safer_eval", false]], "scaleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.ScaleFace", false]], "search() (in module ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.search", false]], "search() (treepattern method)": [[12, "ete4.treematcher.treematcher.TreePattern.search", false]], "search_ancestors() (tree method)": [[11, "ete4.Tree.search_ancestors", false]], "search_descendants() (tree method)": [[11, "ete4.Tree.search_descendants", false]], "search_leaves_by_name() (tree method)": [[11, "ete4.Tree.search_leaves_by_name", false]], "search_nodes() (tree method)": [[11, "ete4.Tree.search_nodes", false]], "search_to_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.search_to_selection", false]], "searches (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.searches", false]], "selected (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.selected", false]], "selected_face (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face", false]], "selected_face_pos (treestyle property)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle.selected_face_pos", false]], "selectedcircleface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedCircleFace", false]], "selectedface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedFace", false]], "selectedrectface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SelectedRectFace", false]], "seqface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqFace", false]], "seqgroup (class in ete4.core.seqgroup)": [[8, "ete4.core.seqgroup.SeqGroup", false]], "seqmotifface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.SeqMotifFace", false]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function", false]], "set_midpoint_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_midpoint_outgroup", false]], "set_node_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_node_style", false]], "set_node_style() (layoutautoname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName.set_node_style", false]], "set_node_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_node_style", false]], "set_node_style() (layoutcuratedname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName.set_node_style", false]], "set_node_style() (layoutetediffdistance method)": [[9, "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance.set_node_style", false]], "set_node_style() (layouteukogs method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs.set_node_style", false]], "set_node_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_node_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_node_style", false]], "set_node_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_node_style", false]], "set_node_style() (layouthumanogs method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs.set_node_style", false]], "set_node_style() (layoutlastcommonancestor method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor.set_node_style", false], [9, "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor.set_node_style", false]], "set_node_style() (layoutleafname method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName.set_node_style", false]], "set_node_style() (layoutnumberleaves method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves.set_node_style", false]], "set_node_style() (layoutoutline method)": [[9, "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline.set_node_style", false]], "set_node_style() (layoutpreferredname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName.set_node_style", false]], "set_node_style() (layoutsciname method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName.set_node_style", false]], "set_node_style() (layoutseeds method)": [[9, "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds.set_node_style", false]], "set_node_style() (layoutucsc method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC.set_node_style", false]], "set_node_style() (layoutucsctrans method)": [[9, "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans.set_node_style", false]], "set_node_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_node_style", false]], "set_outgroup() (in module ete4.core.operations)": [[5, "ete4.core.operations.set_outgroup", false]], "set_outgroup() (tree method)": [[11, "ete4.Tree.set_outgroup", false]], "set_seq() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.set_seq", false]], "set_species_naming_function() (phylotree method)": [[7, "ete4.PhyloTree.set_species_naming_function", false]], "set_style() (tree method)": [[11, "ete4.Tree.set_style", false]], "set_tree_style() (layoutalignment method)": [[9, "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment.set_tree_style", false]], "set_tree_style() (layoutbarplot method)": [[9, "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot.set_tree_style", false]], "set_tree_style() (layoutevolevents method)": [[9, "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents.set_tree_style", false], [9, "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents.set_tree_style", false]], "set_tree_style() (layoutgenomiccontext method)": [[9, "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext.set_tree_style", false]], "set_tree_style() (treelayout method)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout.set_tree_style", false]], "show() (tree method)": [[11, "ete4.Tree.show", false]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette", false]], "size (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.Size", false]], "size (tree attribute)": [[11, "ete4.Tree.size", false]], "skip_quoted_name() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_quoted_name", false]], "skip_spaces_and_comments() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.skip_spaces_and_comments", false]], "sm_style (tree property)": [[11, "ete4.Tree.sm_style", false]], "sort() (in module ete4.core.operations)": [[5, "ete4.core.operations.sort", false]], "sort() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.sort", false]], "sort_descendants() (tree method)": [[11, "ete4.Tree.sort_descendants", false]], "species (phylotree property)": [[7, "ete4.PhyloTree.species", false]], "split_by_dups() (phylotree method)": [[7, "ete4.PhyloTree.split_by_dups", false]], "split_thru_negative_xaxis() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.split_thru_negative_xaxis", false]], "stack() (in module ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.stack", false]], "stackedbarface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.StackedBarFace", false]], "standardize() (tree method)": [[11, "ete4.Tree.standardize", false]], "store_active() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_active", false]], "store_search() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_search", false]], "store_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.store_selection", false]], "style (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.style", false]], "summary() (in module ete4.smartview.renderer.draw_helpers)": [[9, "ete4.smartview.renderer.draw_helpers.summary", false]], "support (tree attribute)": [[11, "ete4.Tree.support", false]], "swap_children() (tree method)": [[11, "ete4.Tree.swap_children", false]], "swap_props() (in module ete4.core.operations)": [[5, "ete4.core.operations.swap_props", false]], "textface (class in ete4.smartview.renderer.faces)": [[9, "ete4.smartview.renderer.faces.TextFace", false]], "timer (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.timer", false]], "to_dendrogram() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_dendrogram", false]], "to_str() (tree method)": [[11, "ete4.Tree.to_str", false]], "to_ultrametric() (in module ete4.core.operations)": [[5, "ete4.core.operations.to_ultrametric", false]], "to_ultrametric() (tree method)": [[11, "ete4.Tree.to_ultrametric", false]], "touch_and_get() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.touch_and_get", false]], "translate_to_names() (ncbitaxa method)": [[10, "ete4.NCBITaxa.translate_to_names", false]], "traverse() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse", false]], "traverse() (tree method)": [[11, "ete4.Tree.traverse", false]], "traverse_bfs() (in module ete4.core.operations)": [[5, "ete4.core.operations.traverse_bfs", false]], "tree (class in ete4)": [[11, "ete4.Tree", false]], "tree (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.tree", false]], "treeactive (class in ete4.smartview.renderer.drawer)": [[9, "ete4.smartview.renderer.drawer.TreeActive", false]], "treedata (class in ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.TreeData", false]], "treelayout (class in ete4.smartview.renderer.treelayout)": [[9, "ete4.smartview.renderer.treelayout.TreeLayout", false]], "treepattern (class in ete4.treematcher.treematcher)": [[12, "ete4.treematcher.treematcher.TreePattern", false]], "treestyle (class in ete4.smartview.renderer.treestyle)": [[9, "ete4.smartview.renderer.treestyle.TreeStyle", false]], "treeview": [[13, "module-treeview", false]], "type (drawer attribute)": [[9, "ete4.smartview.renderer.drawer.Drawer.TYPE", false]], "type (drawercirc attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerCirc.TYPE", false]], "type (drawerrect attribute)": [[9, "ete4.smartview.renderer.drawer.DrawerRect.TYPE", false]], "ultrametric (treedata attribute)": [[9, "ete4.smartview.gui.server.TreeData.ultrametric", false]], "unquote() (in module ete4.parser.newick)": [[6, "ete4.parser.newick.unquote", false]], "unroot() (in module ete4.core.operations)": [[5, "ete4.core.operations.unroot", false]], "unroot() (tree method)": [[11, "ete4.Tree.unroot", false]], "unselect_node() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.unselect_node", false]], "up (tree attribute)": [[11, "ete4.Tree.up", false]], "update_app_available_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_app_available_layouts", false]], "update_layouts() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_layouts", false]], "update_node_props() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_props", false]], "update_node_style() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_node_style", false]], "update_selection() (in module ete4.smartview.gui.server)": [[9, "ete4.smartview.gui.server.update_selection", false]], "update_size() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_size", false]], "update_sizes_all() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_all", false]], "update_sizes_from() (in module ete4.core.operations)": [[5, "ete4.core.operations.update_sizes_from", false]], "update_taxonomy_database() (gtdbtaxa method)": [[10, "ete4.GTDBTaxa.update_taxonomy_database", false]], "update_taxonomy_database() (ncbitaxa method)": [[10, "ete4.NCBITaxa.update_taxonomy_database", false]], "walk() (in module ete4.core.operations)": [[5, "ete4.core.operations.walk", false]], "walker (class in ete4.core.operations)": [[5, "ete4.core.operations.Walker", false]], "write() (phylotree method)": [[7, "ete4.PhyloTree.write", false]], "write() (seqgroup method)": [[8, "ete4.core.seqgroup.SeqGroup.write", false]], "write() (tree method)": [[11, "ete4.Tree.write", false]], "x (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.x", false]], "x (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.x", false]], "y (box attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Box.y", false]], "y (padding attribute)": [[9, "ete4.smartview.renderer.draw_helpers.Padding.y", false]]}, "objects": {"": [[13, 4, 0, "-", "treeview"]], "ete4": [[10, 0, 1, "", "GTDBTaxa"], [10, 0, 1, "", "NCBITaxa"], [7, 0, 1, "", "PhyloTree"], [11, 0, 1, "", "Tree"]], "ete4.GTDBTaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_name_lineage"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.NCBITaxa": [[10, 1, 1, "", "__init__"], [10, 1, 1, "", "annotate_tree"], [10, 1, 1, "", "get_broken_branches"], [10, 1, 1, "", "get_common_names"], [10, 1, 1, "", "get_descendant_taxa"], [10, 1, 1, "", "get_fuzzy_name_translation"], [10, 1, 1, "", "get_lineage"], [10, 1, 1, "", "get_lineage_translator"], [10, 1, 1, "", "get_name_translator"], [10, 1, 1, "", "get_rank"], [10, 1, 1, "", "get_taxid_translator"], [10, 1, 1, "", "get_topology"], [10, 1, 1, "", "translate_to_names"], [10, 1, 1, "", "update_taxonomy_database"]], "ete4.PhyloTree": [[7, 1, 1, "", "__init__"], [7, 1, 1, "", "annotate_gtdb_taxa"], [7, 1, 1, "", "annotate_ncbi_taxa"], [7, 1, 1, "", "collapse_lineage_specific_expansions"], [7, 1, 1, "", "get_age"], [7, 1, 1, "", "get_age_balanced_outgroup"], [7, 1, 1, "", "get_descendant_evol_events"], [7, 1, 1, "", "get_farthest_oldest_leaf"], [7, 1, 1, "", "get_farthest_oldest_node"], [7, 1, 1, "", "get_my_evol_events"], [7, 1, 1, "", "get_speciation_trees"], [7, 1, 1, "", "get_species"], [7, 1, 1, "", "iter_species"], [7, 1, 1, "", "link_to_alignment"], [7, 1, 1, "", "ncbi_compare"], [7, 1, 1, "", "reconcile"], [7, 1, 1, "", "set_species_naming_function"], [7, 2, 1, "", "species"], [7, 1, 1, "", "split_by_dups"], [7, 1, 1, "", "write"]], "ete4.Tree": [[11, 1, 1, "", "__init__"], [11, 1, 1, "", "add_child"], [11, 1, 1, "", "add_children"], [11, 1, 1, "", "add_face"], [11, 1, 1, "", "add_face_smartview"], [11, 1, 1, "", "add_face_treeview"], [11, 1, 1, "", "add_feature"], [11, 1, 1, "", "add_features"], [11, 1, 1, "", "add_prop"], [11, 1, 1, "", "add_props"], [11, 1, 1, "", "add_sister"], [11, 1, 1, "", "ancestors"], [11, 1, 1, "", "check_monophyly"], [11, 3, 1, "", "children"], [11, 3, 1, "", "collapsed_faces"], [11, 1, 1, "", "common_ancestor"], [11, 1, 1, "", "compare"], [11, 1, 1, "", "cophenetic_matrix"], [11, 1, 1, "", "copy"], [11, 1, 1, "", "del_feature"], [11, 1, 1, "", "del_prop"], [11, 1, 1, "", "delete"], [11, 1, 1, "", "descendants"], [11, 1, 1, "", "describe"], [11, 1, 1, "", "detach"], [11, 3, 1, "", "dist"], [11, 1, 1, "", "edges"], [11, 1, 1, "", "expand_polytomies"], [11, 1, 1, "", "explore"], [11, 3, 1, "", "faces"], [11, 1, 1, "", "from_parent_child_table"], [11, 1, 1, "", "from_skbio"], [11, 1, 1, "", "get_cached_content"], [11, 1, 1, "", "get_children"], [11, 1, 1, "", "get_closest_leaf"], [11, 1, 1, "", "get_distance"], [11, 1, 1, "", "get_farthest_leaf"], [11, 1, 1, "", "get_farthest_node"], [11, 1, 1, "", "get_midpoint_outgroup"], [11, 1, 1, "", "get_monophyletic"], [11, 1, 1, "", "get_prop"], [11, 1, 1, "", "get_sisters"], [11, 1, 1, "", "get_topology_id"], [11, 3, 1, "", "id"], [11, 2, 1, "", "img_style"], [11, 1, 1, "", "init_from_ete"], [11, 1, 1, "", "init_from_newick"], [11, 2, 1, "", "is_collapsed"], [11, 2, 1, "", "is_initialized"], [11, 3, 1, "", "is_leaf"], [11, 1, 1, "", "is_monophyletic"], [11, 3, 1, "", "is_root"], [11, 1, 1, "", "iter_prepostorder"], [11, 1, 1, "", "ladderize"], [11, 1, 1, "", "leaf_names"], [11, 1, 1, "", "leaves"], [11, 3, 1, "", "level"], [11, 1, 1, "", "lineage"], [11, 3, 1, "", "name"], [11, 1, 1, "", "pop_child"], [11, 1, 1, "", "populate"], [11, 3, 1, "", "props"], [11, 1, 1, "", "prune"], [11, 1, 1, "", "remove_child"], [11, 1, 1, "", "remove_children"], [11, 1, 1, "", "remove_sister"], [11, 1, 1, "", "render"], [11, 1, 1, "", "resolve_polytomy"], [11, 1, 1, "", "reverse_children"], [11, 1, 1, "", "robinson_foulds"], [11, 3, 1, "", "root"], [11, 1, 1, "", "search_ancestors"], [11, 1, 1, "", "search_descendants"], [11, 1, 1, "", "search_leaves_by_name"], [11, 1, 1, "", "search_nodes"], [11, 1, 1, "", "set_outgroup"], [11, 1, 1, "", "set_style"], [11, 1, 1, "", "show"], [11, 3, 1, "", "size"], [11, 2, 1, "", "sm_style"], [11, 1, 1, "", "sort_descendants"], [11, 1, 1, "", "standardize"], [11, 3, 1, "", "support"], [11, 1, 1, "", "swap_children"], [11, 1, 1, "", "to_str"], [11, 1, 1, "", "to_ultrametric"], [11, 1, 1, "", "traverse"], [11, 1, 1, "", "unroot"], [11, 3, 1, "", "up"], [11, 1, 1, "", "write"]], "ete4.clustering": [[4, 4, 0, "-", "clustertree"]], "ete4.clustering.clustertree": [[4, 0, 1, "", "ClusterTree"]], "ete4.clustering.clustertree.ClusterTree": [[4, 1, 1, "", "__init__"], [4, 2, 1, "", "deviation"], [4, 1, 1, "", "get_dunn"], [4, 1, 1, "", "get_silhouette"], [4, 2, 1, "", "intercluster_dist"], [4, 2, 1, "", "intracluster_dist"], [4, 1, 1, "", "leaf_profiles"], [4, 1, 1, "", "link_to_arraytable"], [4, 2, 1, "", "profile"], [4, 1, 1, "", "set_distance_function"], [4, 2, 1, "", "silhouette"]], "ete4.core": [[5, 4, 0, "-", "operations"], [8, 4, 0, "-", "seqgroup"]], "ete4.core.operations": [[5, 0, 1, "", "Walker"], [5, 5, 1, "", "add_branch_values"], [5, 5, 1, "", "add_leaf_names"], [5, 5, 1, "", "assert_root_consistency"], [5, 5, 1, "", "common_ancestor"], [5, 5, 1, "", "create_dichotomic_sister"], [5, 5, 1, "", "farthest"], [5, 5, 1, "", "farthest_descendant"], [5, 5, 1, "", "insert_intermediate"], [5, 5, 1, "", "interchange_references"], [5, 5, 1, "", "join_branch"], [5, 5, 1, "", "ladderize"], [5, 5, 1, "", "make_name"], [5, 5, 1, "", "midpoint"], [5, 5, 1, "", "move"], [5, 5, 1, "", "populate"], [5, 5, 1, "", "populate_uniform"], [5, 5, 1, "", "populate_yule"], [5, 5, 1, "", "rehang"], [5, 5, 1, "", "remove"], [5, 5, 1, "", "resolve_polytomy"], [5, 5, 1, "", "root_at"], [5, 5, 1, "", "set_midpoint_outgroup"], [5, 5, 1, "", "set_outgroup"], [5, 5, 1, "", "sort"], [5, 5, 1, "", "swap_props"], [5, 5, 1, "", "to_dendrogram"], [5, 5, 1, "", "to_ultrametric"], [5, 5, 1, "", "traverse"], [5, 5, 1, "", "traverse_bfs"], [5, 5, 1, "", "unroot"], [5, 5, 1, "", "update_size"], [5, 5, 1, "", "update_sizes_all"], [5, 5, 1, "", "update_sizes_from"], [5, 5, 1, "", "walk"]], "ete4.core.operations.Walker": [[5, 1, 1, "", "add_next_branch"], [5, 2, 1, "", "first_visit"], [5, 1, 1, "", "go_back"], [5, 2, 1, "", "has_unvisited_branches"], [5, 2, 1, "", "node"], [5, 2, 1, "", "node_id"]], "ete4.core.seqgroup": [[8, 0, 1, "", "SeqGroup"]], "ete4.core.seqgroup.SeqGroup": [[8, 1, 1, "", "__init__"], [8, 1, 1, "", "get_entries"], [8, 1, 1, "", "get_seq"], [8, 1, 1, "", "iter_entries"], [8, 1, 1, "", "set_seq"], [8, 1, 1, "", "write"]], "ete4.parser": [[6, 4, 0, "-", "newick"], [6, 4, 0, "-", "nexus"]], "ete4.parser.newick": [[6, 6, 1, "", "NewickError"], [6, 5, 1, "", "content_repr"], [6, 5, 1, "", "dump"], [6, 5, 1, "", "dumps"], [6, 5, 1, "", "error"], [6, 5, 1, "", "get_extended_props"], [6, 5, 1, "", "get_props"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"], [6, 5, 1, "", "make_parser"], [6, 5, 1, "", "prop_repr"], [6, 5, 1, "", "quote"], [6, 5, 1, "", "read_content"], [6, 5, 1, "", "read_nodes"], [6, 5, 1, "", "repr_short"], [6, 5, 1, "", "skip_quoted_name"], [6, 5, 1, "", "skip_spaces_and_comments"], [6, 5, 1, "", "unquote"]], "ete4.parser.nexus": [[6, 6, 1, "", "NexusError"], [6, 5, 1, "", "apply_translations"], [6, 5, 1, "", "get_commands"], [6, 5, 1, "", "get_section"], [6, 5, 1, "", "get_sections"], [6, 5, 1, "", "get_trees"], [6, 5, 1, "", "load"], [6, 5, 1, "", "loads"]], "ete4.phylo": [[7, 0, 1, "", "EvolEvent"]], "ete4.smartview.gui": [[9, 4, 0, "-", "server"]], "ete4.smartview.gui.server": [[9, 0, 1, "", "GlobalStuff"], [9, 0, 1, "", "TreeData"], [9, 5, 1, "", "activate_clade"], [9, 5, 1, "", "activate_node"], [9, 5, 1, "", "add_tree"], [9, 5, 1, "", "add_trees_from_request"], [9, 5, 1, "", "callback"], [9, 5, 1, "", "change_selection_name"], [9, 5, 1, "", "copy_style"], [9, 5, 1, "", "deactivate_clade"], [9, 5, 1, "", "deactivate_node"], [9, 5, 1, "", "del_tree"], [9, 5, 1, "", "find_node"], [9, 5, 1, "", "get_active_clade"], [9, 5, 1, "", "get_active_clades"], [9, 5, 1, "", "get_command_search"], [9, 5, 1, "", "get_drawer"], [9, 5, 1, "", "get_eval_search"], [9, 5, 1, "", "get_layouts"], [9, 5, 1, "", "get_layouts_from_getters"], [9, 5, 1, "", "get_newick"], [9, 5, 1, "", "get_next_available_port"], [9, 5, 1, "", "get_nodes_info"], [9, 5, 1, "", "get_parents"], [9, 5, 1, "", "get_parser"], [9, 5, 1, "", "get_search_function"], [9, 5, 1, "", "get_selection_info"], [9, 5, 1, "", "get_selections"], [9, 5, 1, "", "get_stats"], [9, 5, 1, "", "get_tid"], [9, 5, 1, "", "get_topological_search"], [9, 5, 1, "", "get_trees_from_file"], [9, 5, 1, "", "get_trees_from_form"], [9, 5, 1, "", "get_trees_from_nexus_or_newick"], [9, 5, 1, "", "initialize"], [9, 5, 1, "", "initialize_tree_style"], [9, 5, 1, "", "json_error"], [9, 5, 1, "", "load_tree"], [9, 5, 1, "", "load_tree_from_newick"], [9, 5, 1, "", "maintenance"], [9, 5, 1, "", "make_name"], [9, 5, 1, "", "nice_html"], [9, 5, 1, "", "open_browser_window"], [9, 5, 1, "", "prune_by_selection"], [9, 5, 1, "", "remove_active"], [9, 5, 1, "", "remove_active_clade"], [9, 5, 1, "", "remove_search"], [9, 5, 1, "", "remove_selection"], [9, 5, 1, "", "req_json"], [9, 5, 1, "", "retrieve_layouts"], [9, 5, 1, "", "retrieve_tree_data"], [9, 5, 1, "", "run_smartview"], [9, 5, 1, "", "safer_eval"], [9, 5, 1, "", "search_to_selection"], [9, 5, 1, "", "sort"], [9, 5, 1, "", "store_active"], [9, 5, 1, "", "store_search"], [9, 5, 1, "", "store_selection"], [9, 5, 1, "", "touch_and_get"], [9, 5, 1, "", "unselect_node"], [9, 5, 1, "", "update_app_available_layouts"], [9, 5, 1, "", "update_layouts"], [9, 5, 1, "", "update_node_props"], [9, 5, 1, "", "update_node_style"], [9, 5, 1, "", "update_selection"]], "ete4.smartview.gui.server.TreeData": [[9, 1, 1, "", "__init__"], [9, 3, 1, "", "active"], [9, 3, 1, "", "exclude_props"], [9, 3, 1, "", "include_props"], [9, 3, 1, "", "initialized"], [9, 3, 1, "", "layouts"], [9, 3, 1, "", "name"], [9, 3, 1, "", "nodestyles"], [9, 3, 1, "", "searches"], [9, 3, 1, "", "selected"], [9, 3, 1, "", "style"], [9, 3, 1, "", "timer"], [9, 3, 1, "", "tree"], [9, 3, 1, "", "ultrametric"]], "ete4.smartview.renderer": [[9, 4, 0, "-", "draw_helpers"], [9, 4, 0, "-", "drawer"], [9, 4, 0, "-", "face_positions"], [9, 4, 0, "-", "faces"], [9, 4, 0, "-", "nodestyle"], [9, 4, 0, "-", "treelayout"], [9, 4, 0, "-", "treestyle"]], "ete4.smartview.renderer.draw_helpers": [[9, 0, 1, "", "Box"], [9, 0, 1, "", "Padding"], [9, 5, 1, "", "cartesian"], [9, 5, 1, "", "circumasec"], [9, 5, 1, "", "circumrect"], [9, 5, 1, "", "clip_angles"], [9, 5, 1, "", "draw_arc"], [9, 5, 1, "", "draw_array"], [9, 5, 1, "", "draw_arrow"], [9, 5, 1, "", "draw_circle"], [9, 5, 1, "", "draw_ellipse"], [9, 5, 1, "", "draw_html"], [9, 5, 1, "", "draw_img"], [9, 5, 1, "", "draw_line"], [9, 5, 1, "", "draw_nodebox"], [9, 5, 1, "", "draw_outline"], [9, 5, 1, "", "draw_rect"], [9, 5, 1, "", "draw_rhombus"], [9, 5, 1, "", "draw_slice"], [9, 5, 1, "", "draw_text"], [9, 5, 1, "", "draw_triangle"], [9, 5, 1, "", "first_value"], [9, 5, 1, "", "get_line_type"], [9, 5, 1, "", "get_xs"], [9, 5, 1, "", "get_ys"], [9, 5, 1, "", "intersects_angles"], [9, 5, 1, "", "intersects_box"], [9, 5, 1, "", "intersects_segment"], [9, 5, 1, "", "split_thru_negative_xaxis"], [9, 5, 1, "", "summary"]], "ete4.smartview.renderer.draw_helpers.Box": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"], [9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.draw_helpers.Padding": [[9, 3, 1, "", "x"], [9, 3, 1, "", "y"]], "ete4.smartview.renderer.drawer": [[9, 0, 1, "", "Active"], [9, 0, 1, "", "Drawer"], [9, 0, 1, "", "DrawerAlignCircFaces"], [9, 0, 1, "", "DrawerAlignRectFaces"], [9, 0, 1, "", "DrawerCirc"], [9, 0, 1, "", "DrawerCircFaces"], [9, 0, 1, "", "DrawerRect"], [9, 0, 1, "", "DrawerRectFaces"], [9, 0, 1, "", "Size"], [9, 0, 1, "", "TreeActive"], [9, 5, 1, "", "dist"], [9, 5, 1, "", "drawn_size"], [9, 5, 1, "", "get_asec"], [9, 5, 1, "", "get_drawers"], [9, 5, 1, "", "get_empty_active"], [9, 5, 1, "", "get_rect"], [9, 5, 1, "", "make_box"], [9, 5, 1, "", "safe_string"], [9, 5, 1, "", "stack"]], "ete4.smartview.renderer.drawer.Active": [[9, 3, 1, "", "parents"], [9, 3, 1, "", "results"]], "ete4.smartview.renderer.drawer.Drawer": [[9, 3, 1, "", "COLLAPSE_SIZE"], [9, 3, 1, "", "MIN_SIZE"], [9, 3, 1, "", "NPANELS"], [9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "draw_aligned_headers"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_content"], [9, 1, 1, "", "draw_node"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_active_children"], [9, 1, 1, "", "get_collapsed_node"], [9, 1, 1, "", "get_outline"], [9, 1, 1, "", "get_popup_props"], [9, 1, 1, "", "get_selected_children"], [9, 1, 1, "", "is_fully_collapsed"], [9, 1, 1, "", "on_first_visit"], [9, 1, 1, "", "on_last_visit"]], "ete4.smartview.renderer.drawer.DrawerAlignCircFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerAlignRectFaces": [[9, 3, 1, "", "NPANELS"]], "ete4.smartview.renderer.drawer.DrawerCirc": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "__init__"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "flush_outline"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerCircFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.DrawerRect": [[9, 3, 1, "", "TYPE"], [9, 1, 1, "", "content_size"], [9, 1, 1, "", "draw_childrenline"], [9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_lengthline"], [9, 1, 1, "", "draw_nodebox"], [9, 1, 1, "", "draw_nodedot"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "in_viewport"], [9, 1, 1, "", "is_small"], [9, 1, 1, "", "node_size"]], "ete4.smartview.renderer.drawer.DrawerRectFaces": [[9, 1, 1, "", "draw_collapsed"], [9, 1, 1, "", "draw_node"]], "ete4.smartview.renderer.drawer.Size": [[9, 3, 1, "", "dx"], [9, 3, 1, "", "dy"]], "ete4.smartview.renderer.drawer.TreeActive": [[9, 3, 1, "", "clades"], [9, 3, 1, "", "nodes"]], "ete4.smartview.renderer.face_positions": [[9, 0, 1, "", "AlignedGrid"], [9, 0, 1, "", "Grid"], [9, 5, 1, "", "make_faces"]], "ete4.smartview.renderer.face_positions.AlignedGrid": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.face_positions.Grid": [[9, 1, 1, "", "add_face"]], "ete4.smartview.renderer.faces": [[9, 0, 1, "", "AlignLinkFace"], [9, 0, 1, "", "AlignmentFace"], [9, 0, 1, "", "ArrowFace"], [9, 0, 1, "", "AttrFace"], [9, 0, 1, "", "CircleFace"], [9, 0, 1, "", "Face"], [9, 0, 1, "", "HTMLFace"], [9, 0, 1, "", "ImgFace"], [9, 0, 1, "", "LegendFace"], [9, 0, 1, "", "OutlineFace"], [9, 0, 1, "", "PieChartFace"], [9, 0, 1, "", "RectFace"], [9, 0, 1, "", "ScaleFace"], [9, 0, 1, "", "SelectedCircleFace"], [9, 0, 1, "", "SelectedFace"], [9, 0, 1, "", "SelectedRectFace"], [9, 0, 1, "", "SeqFace"], [9, 0, 1, "", "SeqMotifFace"], [9, 0, 1, "", "StackedBarFace"], [9, 0, 1, "", "TextFace"]], "ete4.smartview.renderer.faces.AlignLinkFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.AlignmentFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_blocks"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "get_seq"]], "ete4.smartview.renderer.faces.ArrowFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"], [9, 2, 1, "", "orientation"]], "ete4.smartview.renderer.faces.AttrFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_content"]], "ete4.smartview.renderer.faces.CircleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.Face": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "compute_fsize"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"], [9, 1, 1, "", "get_content"], [9, 1, 1, "", "in_aligned_viewport"]], "ete4.smartview.renderer.faces.HTMLFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ImgFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.LegendFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.OutlineFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"], [9, 1, 1, "", "get_box"]], "ete4.smartview.renderer.faces.PieChartFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_pie"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.RectFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.ScaleFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SelectedCircleFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SelectedRectFace": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.faces.SeqFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.SeqMotifFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "build_regions"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.faces.StackedBarFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "draw"]], "ete4.smartview.renderer.faces.TextFace": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "compute_bounding_box"], [9, 1, 1, "", "draw"], [9, 1, 1, "", "fits"]], "ete4.smartview.renderer.layouts": [[9, 4, 0, "-", "context_layouts"], [9, 4, 0, "-", "default_layouts"], [9, 4, 0, "-", "domain_layouts"], [9, 4, 0, "-", "eggnog6_layouts"], [9, 4, 0, "-", "etecompare_layouts"], [9, 4, 0, "-", "evocell_layouts"], [9, 4, 0, "-", "evol_events_layouts"], [9, 4, 0, "-", "ncbi_taxonomy_layouts"], [9, 4, 0, "-", "phylocloud_egg5_layouts"], [9, 4, 0, "-", "seq_layouts"], [9, 4, 0, "-", "spongilla_layouts"], [9, 4, 0, "-", "staple_layouts"]], "ete4.smartview.renderer.layouts.context_layouts": [[9, 0, 1, "", "LayoutGenomicContext"]], "ete4.smartview.renderer.layouts.context_layouts.LayoutGenomicContext": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_context"], [9, 1, 1, "", "get_tooltip"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.default_layouts": [[9, 0, 1, "", "LayoutBranchLength"], [9, 0, 1, "", "LayoutBranchSupport"], [9, 0, 1, "", "LayoutLeafName"], [9, 0, 1, "", "LayoutNumberLeaves"], [9, 0, 1, "", "LayoutOutline"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchLength": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutBranchSupport": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutLeafName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutNumberLeaves": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.default_layouts.LayoutOutline": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.domain_layouts": [[9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.domain_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts": [[9, 0, 1, "", "LayoutBestName"], [9, 0, 1, "", "LayoutBigg"], [9, 0, 1, "", "LayoutCard"], [9, 0, 1, "", "LayoutCazy"], [9, 0, 1, "", "LayoutEvolEvents"], [9, 0, 1, "", "LayoutKeggEnzyme"], [9, 0, 1, "", "LayoutKeggModule"], [9, 0, 1, "", "LayoutKeggNumber"], [9, 0, 1, "", "LayoutKeggPathway"], [9, 0, 1, "", "LayoutLastCommonAncestor"], [9, 0, 1, "", "LayoutPdb"], [9, 0, 1, "", "LayoutPfamDomains"], [9, 0, 1, "", "LayoutProteinName"], [9, 0, 1, "", "LayoutScientificName"], [9, 0, 1, "", "LayoutSmartDomains"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBestName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutBigg": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCard": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutCazy": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggEnzyme": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggModule": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggNumber": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutKeggPathway": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPdb": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutPfamDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutProteinName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutScientificName": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.eggnog6_layouts.LayoutSmartDomains": [[9, 1, 1, "", "__init__"]], "ete4.smartview.renderer.layouts.etecompare_layouts": [[9, 0, 1, "", "LayoutEteDiffDistance"]], "ete4.smartview.renderer.layouts.etecompare_layouts.LayoutEteDiffDistance": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts": [[9, 0, 1, "", "LayoutHumanOGs"], [9, 0, 1, "", "LayoutUCSC"], [9, 0, 1, "", "LayoutUCSCtrans"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutHumanOGs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSC": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evocell_layouts.LayoutUCSCtrans": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.evol_events_layouts": [[9, 0, 1, "", "LayoutEvolEvents"]], "ete4.smartview.renderer.layouts.evol_events_layouts.LayoutEvolEvents": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts": [[9, 0, 1, "", "LayoutLastCommonAncestor"]], "ete4.smartview.renderer.layouts.ncbi_taxonomy_layouts.LayoutLastCommonAncestor": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_color"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.phylocloud_egg5_layouts": [[9, 5, 1, "", "get_layout_evoltype"], [9, 5, 1, "", "get_layout_gnames"], [9, 5, 1, "", "get_layout_lca_rects"], [9, 5, 1, "", "get_layout_ogs_egg5"], [9, 5, 1, "", "get_layout_sciname"]], "ete4.smartview.renderer.layouts.seq_layouts": [[9, 0, 1, "", "LayoutAlignment"]], "ete4.smartview.renderer.layouts.seq_layouts.LayoutAlignment": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "get_seq"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts": [[9, 0, 1, "", "LayoutAutoName"], [9, 0, 1, "", "LayoutCuratedName"], [9, 0, 1, "", "LayoutEukOgs"], [9, 0, 1, "", "LayoutPreferredName"], [9, 0, 1, "", "LayoutSciName"], [9, 0, 1, "", "LayoutSeeds"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutAutoName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutCuratedName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutEukOgs": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutPreferredName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSciName": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.spongilla_layouts.LayoutSeeds": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"]], "ete4.smartview.renderer.layouts.staple_layouts": [[9, 0, 1, "", "LayoutBarplot"]], "ete4.smartview.renderer.layouts.staple_layouts.LayoutBarplot": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.nodestyle": [[9, 0, 1, "", "NodeStyle"]], "ete4.smartview.renderer.nodestyle.NodeStyle": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "init"]], "ete4.smartview.renderer.treelayout": [[9, 0, 1, "", "TreeLayout"], [9, 5, 1, "", "cased_name"]], "ete4.smartview.renderer.treelayout.TreeLayout": [[9, 1, 1, "", "__init__"], [9, 1, 1, "", "set_node_style"], [9, 1, 1, "", "set_tree_style"]], "ete4.smartview.renderer.treestyle": [[9, 0, 1, "", "TreeStyle"]], "ete4.smartview.renderer.treestyle.TreeStyle": [[9, 1, 1, "", "__init__"], [9, 2, 1, "", "active_face"], [9, 2, 1, "", "active_face_pos"], [9, 1, 1, "", "add_legend"], [9, 2, 1, "", "aligned_panel_footer"], [9, 2, 1, "", "aligned_panel_header"], [9, 1, 1, "", "get_legend"], [9, 2, 1, "", "selected_face"], [9, 2, 1, "", "selected_face_pos"]], "ete4.treematcher": [[12, 4, 0, "-", "treematcher"]], "ete4.treematcher.treematcher": [[12, 0, 1, "", "TreePattern"], [12, 5, 1, "", "match"], [12, 5, 1, "", "safer_eval"], [12, 5, 1, "", "search"]], "ete4.treematcher.treematcher.TreePattern": [[12, 1, 1, "", "__init__"], [12, 1, 1, "", "match"], [12, 1, 1, "", "search"]]}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "property", "Python property"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "module", "Python module"], "5": ["py", "function", "Python function"], "6": ["py", "exception", "Python exception"]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:property", "3": "py:attribute", "4": "py:module", "5": "py:function", "6": "py:exception"}, "terms": {"": [1, 4, 6, 7, 9, 10, 11, 12, 15, 18, 20], "0": [0, 1, 4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "000000": [16, 20], "0000aa": 20, "0030c1": 16, "008339": 20, "009000": 20, "02": 16, "02x": 20, "046042": 20, "05": 19, "061813": 20, "09": [16, 19], "0f": [9, 16], "0f0f0f": 20, "0x7f7bf87276a0": 9, "1": [1, 4, 5, 6, 7, 9, 10, 11, 12, 15, 17, 18, 19, 20], "10": [0, 1, 8, 9, 16, 18, 19, 20], "100": [1, 11, 16, 19, 20], "1000": [9, 11, 16], "10090": 17, "101": [16, 20], "10395": 11, "105": [11, 16, 20], "106": 16, "106234": 20, "1093": 0, "11": [9, 15, 16, 19], "110": [16, 20], "110769": 20, "117570": 17, "117571": 17, "12": [9, 16, 17, 19, 20], "120": [16, 20], "123": 6, "125": [16, 20], "127": 16, "13": [16, 19], "131567": 17, "1338369": 17, "135135": 11, "14": [17, 20], "1425170": 17, "1437010": 17, "15": [9, 11, 16, 19, 20], "150": [16, 20], "155": [16, 20], "16": [16, 20], "160": [16, 20], "16666666666666666": 16, "1765": 16, "180": 16, "1800": 9, "182035": 20, "183": 20, "19": 16, "190": [16, 20], "191": [16, 20], "1987": 4, "1997": 15, "1_": 19, "2": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "20": [4, 9, 16, 20], "200": [9, 16, 20], "2001": 15, "2007": [7, 15], "2009": 15, "201": [16, 20], "2010": 11, "2011": [7, 15], "2015": 0, "2016": 0, "2021": 16, "2023": 16, "2027025": 11, "204419": 20, "207598": 17, "21": 9, "22": 16, "22default": 16, "24": 16, "25": [16, 20], "250": [16, 20], "255": 20, "2665952": 17, "2665953": 17, "27": [7, 16], "271621": 20, "2759": 17, "279f9009f46bf675e3a890c19191158b": 11, "2813598": 17, "2813599": 17, "284": 16, "29": 16, "2c": 16, "2n": 11, "3": [0, 1, 5, 7, 9, 11, 15, 17, 18, 19, 20], "30": [16, 20], "300": [16, 20], "300613": 20, "3018035": 17, "303": 16, "314146": 17, "314293": 17, "314295": 17, "32523": 17, "32524": 17, "32525": 17, "33154": 17, "33208": 17, "33213": 17, "333333333333333": 16, "33333333333333337": 16, "3333333333333335": 16, "33511": 17, "351": [16, 20], "370": [16, 20], "376913": 17, "38": 7, "3_": 19, "3abranch": 16, "3aleaf": 16, "3d": 0, "3px": 9, "4": [1, 9, 11, 15, 18, 19, 20], "40": 19, "400": 20, "40000000000003": 16, "40674": 17, "42": 11, "420": [16, 20], "45": [7, 16, 17, 20], "5": [1, 4, 9, 11, 15, 16, 18, 19, 20], "50": [1, 6, 16, 19, 20], "5000": [9, 11, 16], "53": 4, "555": 16, "58": 16, "596401": 20, "5b": 16, "5d": 16, "5px": 9, "6": [1, 7, 9, 11, 16, 19, 20], "60": [9, 16, 20], "600": 20, "6000": 9, "600mb": 17, "6072": 17, "629395": 17, "640858": 20, "65": [4, 16, 20], "6b92d6": 9, "7": [1, 9, 11, 16, 19], "70": [9, 16, 20], "700": 9, "72mb": 17, "753230": 20, "76": 15, "7707": 17, "7711": 17, "7742": 17, "7776": 17, "8": [1, 7, 9, 11, 16, 19, 20], "80": [9, 16], "800": 16, "800000": 9, "8287": 17, "83": 17, "85": [16, 20], "8782": 17, "89593": 17, "8d8d8d": 9, "9": [1, 9, 10, 11, 15, 16, 19], "90": [11, 16, 20], "9347": 17, "9443": 17, "945": 11, "9526": 17, "953250": 20, "9598": 17, "9604": 17, "9605": 17, "9606": 17, "964b00": 16, "973467": 20, "9db0cf": 20, "A": [0, 1, 4, 5, 7, 10, 11, 12, 14, 16, 17, 19, 20], "And": [11, 15, 19, 20], "As": [11, 15, 16, 19], "At": 0, "Being": 19, "But": [18, 19], "By": [1, 4, 7, 15, 16, 19], "For": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "If": [1, 5, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "In": [1, 11, 15, 16, 17, 18, 19, 20], "It": [4, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "Its": [5, 7, 19], "No": 20, "Of": [18, 19], "On": 17, "One": [11, 16, 18, 19, 20], "Or": [16, 17, 19, 20], "Such": 19, "That": 19, "The": [0, 1, 5, 7, 9, 10, 11, 12, 15, 16, 17, 18, 20], "Then": 11, "There": [1, 11, 15, 18, 19, 20], "These": [16, 17, 19], "To": [8, 11, 15, 16, 17, 19, 20], "Will": [18, 19], "With": [19, 20], "_": [7, 15, 19], "_0_": 19, "_2_": 19, "__init__": [4, 7, 8, 9, 10, 11, 12, 16, 20], "__main__": 20, "__name__": [11, 20], "_get_collaps": 11, "_get_initi": 11, "_get_sm_styl": 11, "_get_styl": 11, "a1": [9, 16, 20], "a2": [9, 16, 20], "a3": [16, 20], "a4": 20, "a50000": 9, "aa": [9, 16, 19], "aa0000": 20, "aaaaaaaaaaa": 8, "ab": [4, 16, 19], "abc": 6, "abc_layout": 20, "abcd": 19, "abcdefghijklmnopqrstuvwxyz": 5, "abl": [1, 16, 18, 19], "abort": 9, "about": [2, 7, 9, 15, 16, 18, 19, 20], "abov": [15, 16, 17, 19, 20], "absolut": [11, 15], "accept": [6, 11, 16, 17, 18, 19, 20], "access": [7, 15, 16, 17, 19, 20], "accord": [5, 6, 7, 9, 11, 15, 19, 20], "accur": 0, "acept": 4, "across": 1, "act": [16, 20], "action": [16, 19], "activ": [9, 16], "activate_clad": 9, "activate_nod": 9, "active_children": 9, "active_fac": 9, "active_face_po": 9, "active_layout": 9, "active_nod": 9, "actual": [1, 19], "acycl": 19, "ad": [7, 10, 11, 14, 16, 17, 19, 20], "adapt": [16, 17], "add": [1, 4, 5, 7, 8, 9, 10, 11, 17, 19], "add_branch_valu": [3, 5], "add_child": [11, 19], "add_children": 11, "add_fac": [9, 11, 16, 20], "add_face_smartview": 11, "add_face_to_nod": [1, 20], "add_face_treeview": 11, "add_featur": 11, "add_leaf_nam": [3, 5], "add_legend": [9, 16], "add_next_branch": 5, "add_prop": [11, 16, 17, 19, 20], "add_sist": [11, 19], "add_tre": 9, "add_trees_from_request": 9, "addit": [16, 17, 18, 19], "addition": [15, 19], "adh1": 19, "adh2": 19, "adh3": 19, "adh4": 19, "adhi": 19, "adhx": 19, "adjac": 20, "adjust": [15, 16, 20], "adress": 11, "advance_layout": 16, "advantag": [16, 20], "aeiou": 19, "affect": [10, 15, 19, 20], "after": [6, 7, 11, 15, 16, 19, 20], "ag": [7, 15], "again": [1, 15, 18, 19], "age2nam": 15, "agp": 0, "ahtpssldtphfvfqtykmgapplppstaapvgqgarqddssssaspsvqgaprevvdpsggwatllesir": [16, 20], "aid": 4, "aim": 15, "ajmonlin": 11, "al": 15, "alg": 15, "alg_format": [7, 15], "algorithm": [7, 16, 19], "alia": 9, "align": [0, 2, 3, 7, 9, 11, 14, 20], "aligned_fac": [9, 16], "aligned_panel_foot": [9, 16], "aligned_panel_head": [9, 16], "alignedgrid": 9, "alignlinkfac": 9, "alignmentfac": [9, 16], "all": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 20], "all_act": 16, "all_select": 16, "allow": [1, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "almost": 1, "aln": 16, "along": 19, "alqeklkdfpvcvstkpepeddaeeglgglpsn": [16, 20], "alreadi": [17, 18, 19, 20], "also": [4, 7, 9, 10, 11, 15, 17, 18, 19, 20], "altern": [8, 10, 15, 19], "although": [15, 16, 19, 20], "altnvsh": 15, "altnvshnia": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeah": 15, "altnvshniavqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "altnvshniavqylsefgtddqpdrreeah": 15, "alwai": [11, 15, 18, 19], "amniota": 17, "among": [11, 15, 16, 19], "an": [5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "analogi": 19, "analys": [0, 15, 19, 20], "analysi": [0, 4, 15, 16, 19, 20], "analyz": [4, 19], "ancestor": [5, 9, 10, 11, 16], "ancestor_a": 16, "ancestor_b": 16, "ancestor_c": 16, "ancestor_d": 16, "ancestor_jfc": 19, "ancestr": 15, "anchor": 9, "anchor_stroke_color": 9, "anchor_stroke_width": 9, "ancylobact": 17, "angl": 9, "ani": [1, 5, 6, 9, 10, 11, 15, 16, 17, 18, 19, 20], "annot": [0, 7, 10, 14], "annotate_dict": 17, "annotate_gtdb_taxa": [7, 17], "annotate_ncbi_taxa": [7, 17], "annotate_tre": 10, "annular": 9, "anoth": [11, 16, 19], "answer": 17, "ap": 20, "apart": 20, "aperlqeygsiftda": [16, 20], "api": [0, 9], "app": 9, "appear": [9, 11, 15, 16, 19], "append": [16, 19], "appl": 4, "appli": [15, 16, 17, 19, 20], "applic": 15, "apply_transl": 6, "approach": [15, 17, 19], "appropri": [9, 12, 15], "aqak": [16, 20], "aquaticu": 17, "ar": [4, 7, 8, 10, 11, 12, 15, 16, 17, 18, 19, 20], "arbitrari": [5, 11, 18, 20], "arbitrarili": 19, "arc": 9, "arc_span": 20, "arc_start": 20, "arc_typ": 9, "area": [16, 20], "arg": [6, 9, 20], "argument": [4, 6, 7, 10, 15, 16, 19, 20], "arial": [16, 20], "around": [16, 20], "arrai": [4, 9, 11, 16], "arrayt": 4, "arraytbl": 4, "arrow": 9, "arrow_typ": 9, "arrowfac": 9, "ascii": 11, "asec": 9, "ask": [2, 15], "aspect": 14, "assert_root_consist": [3, 5], "assertionerror": 5, "assign": [7, 9, 11, 15, 17], "assist": [15, 19], "associ": [0, 4, 7, 8, 10, 11, 15, 17], "assum": [1, 7, 19], "attach": [11, 15, 16, 20], "attempt": 17, "attr": 9, "attrfac": [1, 9, 20], "attribut": [9, 10, 11, 14, 15, 16, 17, 20], "attributt": 16, "auto": 9, "autodetect": 15, "autodetect_dupl": [7, 15], "autom": [0, 19], "automat": [1, 7, 9, 11, 14, 18, 19, 20], "av": 17, "avail": [7, 9, 11, 15, 16, 19, 20], "averag": 19, "avocado": 0, "avoid": [7, 8, 16, 19], "avrilom": 0, "awar": [0, 15], "b": [1, 4, 5, 11, 16, 17, 18, 19, 20], "b1": [9, 16, 20], "b2": [9, 16, 20], "b3": [16, 20], "b4": [16, 20], "backbon": 16, "background": 15, "bacpathgenom": 0, "bacteria": 17, "bacteriovorax": 17, "bacteriovoru": 17, "balanc": [7, 11, 19], "bar": [6, 9], "barcelona": 0, "barplot": 16, "barplot_layout": 16, "basal": 19, "base": [4, 7, 9, 11, 15, 17, 19, 20], "basic": [1, 7, 14, 15, 16, 20], "bcc3d0": [9, 16], "bda": 9, "bda0": 9, "bda1": 9, "bdellovibrio": 17, "bdellovibrionota": 17, "bdr": 9, "bdx": 9, "bdy": 9, "bdy0": 9, "bdy1": 9, "becaus": [15, 16], "becom": 19, "been": [4, 15], "befor": [11, 16, 18, 19, 20], "beforehand": 18, "begin": 19, "behavior": 15, "behind": 11, "being": [11, 15, 19], "belong": [15, 20], "below": [16, 19, 20], "benefit": 15, "besid": 15, "best": [9, 10, 15, 18, 20], "best_nam": 9, "better": [7, 19], "between": [5, 7, 11, 14, 15, 16], "bf": 11, "bgcolor": [9, 16, 20], "bifurc": 19, "bigg": 9, "bigger": 16, "biggest": 5, "bilateria": 17, "binari": 11, "bio": 11, "bioinformat": [0, 7, 19], "biol": [0, 7], "biologi": [0, 15], "biped": 20, "black": [9, 16, 19, 20], "blank": [16, 20], "blog": 0, "blue": [9, 16, 20], "bold": 20, "bool": [7, 9, 11], "boolean": 19, "bootstrap": 19, "border": [16, 20], "boreoeutheria": 17, "bork": 0, "both": [11, 15, 16, 19, 20], "bottl": 16, "bottom": [11, 16, 20], "bottom_textfac": 16, "bottommost": 19, "bound": 9, "boundingrect": 20, "box": [9, 16], "box1": 9, "box2": 9, "box_motif": [16, 20], "bprop": [5, 11], "bracket": 19, "branch": [5, 9, 10, 11, 14, 15], "branch_bottom": [9, 11, 16], "branch_right": [9, 11, 16], "branch_top": [9, 11, 16], "branch_vertical_margin": 20, "breadth": [5, 11], "break": 20, "brief": 0, "brother": 19, "brown": [16, 20], "brows": [2, 14], "browser": [9, 16], "btext": 9, "bubble_map": 20, "build": [0, 9], "build_block": 9, "build_region": 9, "built": [15, 16, 19, 20], "bunch": 11, "button": 16, "bye": 18, "c": [1, 4, 5, 11, 16, 18, 19, 20], "c1": [16, 20], "c2": [16, 20], "c3": [16, 20], "c43b5d": 9, "c__korarchaeia": 17, "c__peptococcia": 17, "c__thorarchaeia": 10, "cach": [11, 14, 18], "cached_cont": [7, 11], "calcul": [4, 7, 10, 11, 15, 19], "call": [1, 9, 11, 12, 15, 16, 17, 18, 19, 20], "callback": 9, "can": [4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20], "cani": [15, 20], "canida": 20, "cannot": 19, "cansnper": 0, "card": 9, "care": 19, "cartesian": 9, "cascad": 11, "case": [1, 11, 15, 16, 19, 20], "cased_nam": 9, "catarrhini": 17, "categori": 15, "cazi": 9, "cbgp": 0, "cccccc": 20, "cd": 19, "cellular": 17, "center": [5, 9, 20], "centroid": 4, "cepa": [0, 7, 15], "certain": [15, 19], "cfa": [15, 20], "cfa_001": 15, "ch": [16, 18], "chang": [1, 5, 6, 11, 15, 16, 18, 19], "change_selection_nam": 9, "char": [5, 8], "charact": [6, 15], "charleston": 15, "check": [1, 11, 14, 15, 16, 18, 20], "check_interv": 9, "check_monophyli": [11, 19], "child": [5, 7, 10, 11, 19], "child_idx": 11, "child_po": 5, "children": [4, 5, 7, 9, 11, 12, 16, 18, 19, 20], "chimp": [15, 20], "chimp_1": 15, "chimp_2": 15, "chimp_3": 15, "chimpa": 15, "chimpanze": 20, "chimpb": 15, "chimpc": 15, "chimpfac": 20, "choos": [16, 20], "chordata": 17, "chosen": 7, "cipf": 0, "circ": 9, "circl": [9, 16, 20], "circle_typ": 9, "circlefac": [9, 16, 20], "circular": [9, 16, 19], "circular_styl": 20, "circumasec": 9, "circumfer": 20, "circumrect": 9, "circumscrib": 9, "citat": [0, 4, 7, 17], "citrobact": 16, "clade": [9, 17], "clade_typ": 11, "class": [2, 3, 4, 5, 7, 8, 9, 10, 12, 15, 16, 17, 18, 19, 20], "classif": [0, 17], "classifi": 0, "click": 16, "climateecologi": 0, "clip": [16, 20], "clip_angl": 9, "clock": 20, "clonal": 0, "clone": [11, 19], "closest": 11, "cluster": [2, 3, 19], "clustertre": [3, 4], "code": [1, 5, 7, 9, 11, 12, 15, 16, 17, 19, 20], "code2desc": 20, "code2nam": [15, 20], "col": [9, 20], "collaps": [7, 9, 10, 11], "collapse_by_conserv": 9, "collapse_conserv": 9, "collapse_lineage_specific_expans": [7, 15], "collapse_s": [9, 16], "collapse_subspeci": [10, 17], "collapsed_fac": 11, "collapsed_id": [9, 16], "collapsed_leaf": 19, "collapsed_nod": 9, "collapsed_onli": [9, 11, 16], "collapsing_height": 9, "collect": [5, 8, 11, 16, 19, 20], "colloqui": 20, "color": [9, 19, 20], "color_gradi": [9, 16], "color_prop": 9, "color_rang": [9, 16], "colormap": [9, 16], "colorsi": 20, "colorstrip": 16, "column": [1, 9, 11, 16, 20], "com": [0, 11, 16, 17], "combin": [11, 14, 15, 17], "combinatori": 15, "combinedlayout_bas": 16, "combinedlayout_object": 16, "comfort": 18, "command": [6, 9, 16, 19], "comment": [6, 8], "common": [5, 7, 9, 10, 11, 15, 16, 18, 20], "common_ancestor": [3, 5, 11, 15, 16, 19, 20], "common_edg": 19, "commonli": [17, 19], "compact": [11, 18, 19], "compact_aln": 16, "compactseq": [16, 20], "compar": [0, 11, 14, 15], "comparison": [0, 15, 19], "compars": 0, "compat": [7, 11, 19], "compil": 18, "complet": [10, 15, 16, 19, 20], "complex": [11, 16, 18, 19], "compon": 16, "comprehens": [17, 19], "compress": [9, 11], "compris": 19, "comput": [0, 4, 9, 11, 19], "compute_bounding_box": 9, "compute_fs": 9, "compute_pi": 9, "concaten": 14, "concept": 19, "conceptu": 19, "condit": [11, 12, 16, 18, 19], "conf": 19, "confer": 0, "confid": 19, "config": [16, 20], "connect": [10, 11, 17, 19], "connector": 10, "conost": 16, "conostant_color": 16, "conostant_node_s": 16, "conostant_textfac": 16, "consequ": 15, "conserv": 11, "conservation_threshold": 9, "consid": [11, 15, 19], "consider": 19, "consist": [11, 16, 17, 19], "consol": 18, "constant": 19, "constraint": 12, "construct": [18, 19], "constructor": [12, 19, 20], "contact": 0, "contain": [7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "container_typ": 11, "content": [4, 6, 7, 11, 14], "content_repr": 6, "content_s": 9, "context": [12, 16, 18], "continu": [16, 20], "contrast": 19, "control": [19, 20], "conveni": [15, 17, 19], "convent": [5, 11, 19], "convers": [17, 20], "convert": [1, 5, 7, 10, 11, 15, 17, 19], "cool": 19, "cophenet": 11, "cophenetic_matrix": 11, "copi": [7, 11, 14, 20], "copy_styl": 9, "copyright": 16, "core": [9, 11, 15], "corner": 16, "correct_by_polytomy_s": 11, "correspond": [5, 6, 7, 9, 10, 15, 18, 19, 20], "correspondig": 15, "could": [1, 4, 11, 15, 16, 18, 19, 20], "count": [16, 19], "count_leav": 9, "courier": 16, "cours": [18, 19], "cover": 7, "cpickl": [11, 19], "craniata": 17, "creat": [1, 4, 5, 9, 11, 12, 15, 16], "create_dichotomic_sist": [3, 5], "credit": 16, "crg": 0, "criteria": [7, 11], "crucial": 19, "cryptofilum": 17, "ctrl": 16, "current": [1, 5, 7, 8, 9, 10, 11, 15, 16, 19], "cursor": 16, "custom": [1, 10, 11, 14, 17], "cut": [9, 11, 19], "cyprinida": 20, "d": [1, 4, 5, 7, 9, 11, 15, 16, 18, 19, 20], "d0d0d0": 9, "d1": 16, "d2": 16, "d__archaea": 17, "d__bacteria": 17, "da": 9, "daili": 17, "danio": 20, "darkr": [16, 20], "darkseagreen": [16, 20], "darwin": 11, "dash": [9, 16, 20], "data": [0, 4, 9, 11, 15, 16, 17, 19, 20], "databas": [0, 2, 3, 7, 14], "date": 14, "dbfile": [7, 10], "deactiv": 16, "deactivate_clad": 9, "deactivate_nod": 9, "deal": [15, 19], "decid": [16, 19], "deepcopi": [11, 19], "deepest": 19, "def": [1, 7, 15, 16, 19, 20], "default": [1, 4, 6, 7, 11, 15, 16, 17, 19, 20], "defin": [9, 15, 17, 18, 19, 20], "definit": 19, "del_featur": 11, "del_prop": [11, 19], "del_tre": 9, "delet": [9, 11], "delete_orphan": 11, "delimit": 0, "demonstr": 16, "dendrochirotida": 17, "dendrogram": 5, "dengzq1234": 16, "denisova": 17, "depart": 0, "depend": [1, 5, 11, 15, 19, 20], "depth": [11, 19], "deriv": [10, 20], "descend": [4, 5, 7, 10, 11, 14, 16, 18], "descfac": 20, "describ": [7, 11, 15, 16, 18], "descript": [1, 4, 9, 11, 16, 19, 20], "design": [19, 20], "detach": 11, "detail": [7, 19, 20], "detect": [1, 7, 11, 14, 17, 19], "determin": [19, 20], "deuterostomia": 17, "develop": 0, "deviat": 4, "df": 11, "diamet": [4, 5, 16, 20], "dichotom": [5, 11], "dichotomi": 5, "dicotom": [5, 11], "dicotomi": [5, 11], "dict": [4, 6, 9, 10, 11, 16], "dictionari": [7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "did": [18, 19], "diff": 9, "diff_node_color": 9, "diff_node_s": 9, "differ": [1, 7, 9, 11, 14, 15, 16, 18, 19, 20], "differenti": 19, "digit": 16, "dimension": 11, "dipnotetrapodomorpha": 17, "diptera": 20, "direct": 15, "directli": [16, 19, 20], "disabl": [15, 19], "discard": 19, "discarded_edges_t1": 11, "discarded_edges_t2": 11, "disconnect": 19, "discret": [9, 16], "displai": 0, "dist": [5, 6, 9, 11, 16, 18, 19, 20], "dist_fn": [5, 11], "distanc": [1, 4, 5, 9, 11, 14, 15], "distant": [15, 19], "distinct": 19, "distinguish": 18, "distribut": 17, "diverg": 15, "divid": 11, "dme": [15, 20], "dme_001": 15, "dme_002": 15, "dmp": 17, "do": [5, 11, 12, 15, 16, 18, 19, 20], "doc": 20, "document": [15, 16, 20], "doe": [1, 10, 12, 15, 17, 18, 19, 20], "doesn": [17, 18], "dog": [15, 20], "dogfac": 20, "doi": 0, "domain_layout": 16, "domest": 20, "don": 5, "done": [6, 15, 16, 19], "dopazo": 7, "dot": [9, 11, 16, 20], "doubl": 11, "down": 19, "download": [10, 15, 17], "downward": 19, "dpi": [11, 20], "draw": [2, 11, 14, 15], "draw_aligned_head": 9, "draw_arc": 9, "draw_arrai": 9, "draw_arrow": 9, "draw_childrenlin": 9, "draw_circl": 9, "draw_collaps": 9, "draw_cont": 9, "draw_descend": [9, 16], "draw_ellips": 9, "draw_html": 9, "draw_img": 9, "draw_lengthlin": 9, "draw_lin": 9, "draw_nod": 9, "draw_nodebox": 9, "draw_nodedot": 9, "draw_outlin": 9, "draw_rect": 9, "draw_rhombu": 9, "draw_slic": 9, "draw_text": [9, 16], "draw_triangl": 9, "drawer": 16, "draweraligncircfac": 9, "draweralignrectfac": 9, "drawercirc": 9, "drawercircfac": 9, "drawerrect": 9, "drawerrectfac": 9, "drawn": [16, 20], "drawn_siz": 9, "dre": 20, "drosophila": [15, 20], "dump": [6, 10, 15, 17], "dunn": 4, "dup": [7, 15], "dup1": 15, "dup2": 15, "dup3": 15, "duplic": [0, 1, 7, 11, 14], "duplication_color": 9, "dure": [16, 20], "dx": [9, 16], "dx_befor": 9, "dx_to_closest_child": 9, "dy": [9, 16], "dy_befor": 9, "dynam": [7, 11, 15, 16, 19, 20], "dynamicitemfac": 20, "e": [0, 1, 5, 9, 10, 11, 16, 18, 19, 20], "e5e5e5": 16, "each": [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "easier": 17, "easiest": [1, 17], "easili": [15, 17, 19, 20], "edg": [11, 16, 19], "edges_t1": 11, "edges_t2": 11, "edit": 16, "editor": 16, "ef": [15, 19], "effect": [8, 11], "effective_tree_s": 19, "effici": [15, 17, 18], "efg": 19, "efgdlnealnsi": 15, "efgdlnealnsyyayqtddqkdrreeah": 15, "efgdlnealnsyyayqtddqkdrreeahqfmaltnvsh": 15, "efgtddqkdrreeah": 15, "eggnog": 0, "either": [9, 17, 19], "element": [1, 9, 11, 16, 19, 20], "elif": [15, 16, 20], "ellips": 20, "ellipse_typ": 9, "els": [1, 16, 17, 19, 20], "embl": 0, "emploi": 17, "empti": [4, 11, 15, 17, 19, 20], "emul": 19, "enabl": [1, 16], "enclos": 19, "encod": [7, 8, 11, 15, 19], "end": [1, 6, 9, 11, 16, 18, 19, 20], "engin": [1, 15, 16, 20], "enhanc": 16, "enjoi": 18, "enorm": 15, "ensur": [16, 20], "entail": 19, "entir": [16, 19], "entiti": 17, "entri": 8, "enumer": 20, "environ": 16, "environment": 17, "enzym": 9, "equal": [16, 19, 20], "equidist": [5, 11, 16], "error": [6, 9, 11, 18], "escap": 6, "escaped_char": 6, "escherichia": 16, "essenti": [16, 17, 19], "establish": [15, 19], "estim": [7, 20], "et": [9, 10, 11, 14, 15, 16, 17, 18, 20], "etc": [11, 16, 18, 20], "ete3": [0, 16], "ete4": [1, 9, 11, 14, 15, 16, 18, 19, 20], "ete4_galleri": 16, "etetoolkit": [0, 17], "etiqqfmaltnvshniavqylsefgdln": 15, "etyp": [7, 15], "euarchontoglir": 17, "euclidean": 4, "euk": 9, "eukaryota": 17, "eumetazoa": 17, "euteleostomi": 17, "eutheria": 17, "ev": 15, "eval": [9, 12, 16], "evalu": [9, 16, 18], "even": [11, 15, 16, 17, 19, 20], "event": [7, 9, 14], "event1": 15, "event2": 15, "everi": [5, 9, 11, 15, 16, 19], "everywher": 9, "evol": 0, "evolev": [3, 15], "evoltyp": [7, 15], "evolutionari": [7, 9, 14, 19], "exact": [5, 10, 15, 19], "exactli": 11, "examin": 19, "exampl": [0, 1, 4, 5, 6, 7, 8, 9, 10, 11, 14, 15, 17, 19, 20], "except": [6, 18, 19], "exclud": [11, 19], "exclude_prop": [9, 11, 16], "exclus": [11, 19], "execut": [16, 20], "exist": [18, 19], "exit": 11, "expand": [11, 19], "expand_polytomi": 11, "expans": [7, 15], "expect": [4, 7, 15, 18, 19], "expected_result": 18, "experi": 1, "experiment": 10, "explain": 15, "explanatori": 19, "explor": [0, 1, 2, 9, 11, 14, 15, 19, 20], "explore_show": 16, "explore_standalon": 16, "exponenti": 11, "export": [19, 20], "express": [9, 12, 14], "extant": 20, "extend": [7, 9, 11, 15, 19], "extens": [1, 11, 15, 20], "extern": [16, 19, 20], "extra": [9, 16, 18, 19, 20], "extract": [6, 9, 17], "extrem": 1, "f": [1, 5, 11, 15, 16, 18, 19, 20], "f__korarchaeacea": 17, "f__tho": 17, "f__thorarchaeacea": 17, "fa8072": 9, "faa": 16, "face": [1, 3, 11, 14], "face1": 9, "face2": 9, "face_grid_tutori": 20, "facecontain": 9, "faceposition_al": 16, "faceposition_align": 16, "faceposition_bottom": 16, "faceposition_collaps": 16, "faceproperties_textfac": 16, "facilit": [17, 19], "fact": 19, "fade": 16, "fals": [1, 5, 7, 9, 10, 11, 12, 15, 16, 19, 20], "famili": [7, 11, 14, 17, 20], "familiar": 19, "familiari": [15, 20], "fanci": 1, "farthest": [3, 5, 7, 11, 15, 19], "farthest_descend": [3, 5], "fast": [0, 19], "fasta": [7, 8, 15, 16], "fasta_txt": 15, "fastafil": 16, "faster": [14, 15], "fb3640": 9, "fdist": 4, "feasibl": 11, "featur": [0, 1, 4, 7, 11, 15, 16, 17, 19, 20], "feel": 18, "fetch": 17, "few": [15, 18], "ff0000": [16, 20], "fgcolor": [9, 16, 20], "field": [9, 16], "file": [1, 4, 6, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "file_nam": 11, "filenam": [1, 9], "fileobject": 9, "filter": [15, 19], "final": [18, 19, 20], "find": [5, 11, 15, 16, 18], "find_nod": 9, "fine": [4, 11], "fir": 15, "first": [5, 7, 9, 10, 11, 15, 16, 17, 18, 20], "first_valu": 9, "first_visit": 5, "fish": [15, 20], "fish_1": 15, "fish_3": 15, "fishfac": 20, "fit": 9, "fix": [11, 15], "fix_dupl": 8, "flag": [11, 15, 19], "flexibl": [1, 19], "fli": 20, "float": [9, 11, 16, 20], "flush_outlin": 9, "fly": [15, 16, 20], "flyfac": 20, "fma": 15, "fmaltnvsh": 15, "fmaltnvshniavqi": 15, "fn": [4, 7], "fname": 17, "fo": 16, "follow": [1, 4, 7, 11, 15, 16, 17, 19, 20], "font": 1, "foo": 6, "footer": [9, 16], "forc": 8, "force_topologi": 1, "foreground": [16, 20], "form": [9, 11, 16], "formal": 19, "format": [4, 6, 7, 8, 9, 10, 11, 15, 17, 19, 20], "format_root_nod": [6, 7, 11], "formatt": [9, 16], "forward": 20, "fould": 11, "found": [4, 7, 15, 16, 18, 19, 20], "foundat": 16, "four": [16, 20], "fp": 6, "frame": 16, "framework": 16, "francoi": 0, "free": [0, 18], "freeli": [18, 19], "frequenc": 16, "frequent": [2, 19], "freshwat": 20, "from": [1, 5, 6, 7, 9, 10, 11, 14, 15, 16, 17, 20], "from_parent_child_t": 11, "from_skbio": 11, "from_skibio": 11, "front": [9, 11], "fseq": 15, "fsize": [1, 20], "ftp": 17, "ftype": [9, 16], "full": [6, 11, 15, 16, 19], "fullfil": 17, "fulli": [16, 17, 20], "function": [1, 4, 5, 7, 9, 11, 15, 17, 18], "fundament": 16, "fungi": 19, "further": 17, "futher": 16, "futur": [5, 11, 17], "g": [1, 6, 11, 16, 18, 19, 20], "g9": 17, "g__b65": 17, "g__jacael01": 17, "g__korarchaeum": 17, "g__mp8t": 17, "g__owc5": 17, "g__shmx01": 17, "g__smtz1": 17, "g__tekir": 17, "g__wtck01": 17, "gabaldon": [7, 15], "gap_format": [9, 16, 20], "gap_linewidth": [9, 16], "gapcolor": [9, 16, 20], "gb_gca_003344655": 17, "gb_gca_003662765": 17, "gb_gca_003662805": 17, "gb_gca_013138615": 17, "gb_gca_020833055": 17, "gdlneal": 15, "gdlnealnsi": 15, "gene": [7, 9, 11, 14], "gene_nam": 9, "gene_tree_nw": 15, "gener": [2, 5, 11, 15, 16, 19, 20], "genes_tre": 19, "genet": 17, "genetre": 15, "genom": [0, 7, 9, 15, 17], "genotyp": 0, "genu": [17, 20], "geometr": [16, 20], "germani": 0, "get": [7, 9, 10, 14, 15, 16, 18], "get_active_children": 9, "get_active_clad": 9, "get_ag": [7, 15], "get_age_balanced_outgroup": 7, "get_asec": 9, "get_background": 16, "get_box": 9, "get_broken_branch": 10, "get_cached_cont": [11, 18, 19], "get_children": 11, "get_closest_leaf": 11, "get_collapsed_nod": 9, "get_color": 9, "get_command": 6, "get_command_search": 9, "get_common_nam": 10, "get_cont": 9, "get_context": 9, "get_descendant_evol_ev": [7, 15], "get_descendant_taxa": [10, 17], "get_descendants_evol_ev": 7, "get_dist": [11, 19], "get_draw": 9, "get_dunn": 4, "get_empty_act": 9, "get_entri": 8, "get_eval_search": 9, "get_example_tre": 20, "get_extended_prop": 6, "get_farthest_leaf": [11, 19], "get_farthest_nod": [11, 19], "get_farthest_oldest_leaf": [7, 15], "get_farthest_oldest_nod": [7, 15], "get_fuzzy_name_transl": 10, "get_heatmapfac": 16, "get_i": 9, "get_layout": 9, "get_layout_evoltyp": 9, "get_layout_gnam": 9, "get_layout_lca_rect": 9, "get_layout_ogs_egg5": 9, "get_layout_scinam": 9, "get_layouts_from_gett": 9, "get_legend": 9, "get_line_typ": 9, "get_lineag": [10, 17], "get_lineage_transl": 10, "get_midpoint_outgroup": [11, 19], "get_monophylet": [11, 19], "get_my_evol_ev": [7, 15], "get_name_lineag": 10, "get_name_transl": [10, 17], "get_newick": 9, "get_next_available_port": 9, "get_node_fac": 16, "get_nodes_info": 9, "get_outlin": 9, "get_par": 9, "get_pars": 9, "get_popup_prop": 9, "get_prop": [6, 11], "get_rank": [10, 17], "get_rect": 9, "get_search_funct": 9, "get_sect": 6, "get_select": 9, "get_selected_children": 9, "get_selection_info": 9, "get_seq": [8, 9, 16], "get_silhouett": 4, "get_sist": 11, "get_speci": [7, 15], "get_speciation_tre": [7, 15], "get_species_nam": 15, "get_stat": 9, "get_taxid_transl": [10, 17], "get_tid": 9, "get_tooltip": 9, "get_topologi": [10, 17], "get_topological_search": 9, "get_topology_id": 11, "get_tre": 6, "get_tree_styl": 16, "get_trees_from_fil": 9, "get_trees_from_form": 9, "get_trees_from_nexus_or_newick": 9, "get_x": 9, "getattr": 18, "gist": 11, "github": [11, 16, 17], "give": 10, "given": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 20], "global": 9, "globalstuff": 9, "glqrrprhriqsk": [16, 20], "gmail": 0, "gnathostomata": 17, "go": [11, 18, 19], "go_back": 5, "goal": 1, "goe": 16, "gold": [16, 20], "googlegroup": 0, "gracefulli": 9, "gradient": 15, "gradient_color": 16, "grai": [9, 16, 20], "grain": [4, 11], "graph": [16, 19, 20], "graphic": [2, 3, 4, 16, 19, 20], "gray_aln": 16, "great": 11, "greatli": 0, "green": [16, 19, 20], "grei": 9, "grid": 9, "group": [0, 7, 10, 11, 15, 19], "grow": [5, 11, 19], "gtdb": [10, 14], "gtdb202dump": 17, "gtdb_spcode": 17, "gtdb_taxonomi": 17, "gtdb_to_taxdump": 17, "gtdbtaxa": [3, 17], "gtdbtaxdump": 10, "gui": [16, 19, 20], "guid": [0, 2], "gz": [10, 17], "h": [1, 7, 11, 15, 16, 18, 19, 20], "ha": [5, 6, 9, 11, 15, 16, 18, 19], "halter": 20, "hampshir": [11, 19], "hand": 17, "handi": 19, "handl": [0, 19, 20], "hang": [5, 11, 19], "haplorrhini": 17, "hard": [5, 11], "has_dupl": 11, "has_unvisited_branch": 5, "have": [5, 10, 11, 15, 16, 18, 19], "head": 16, "header": [9, 11, 16], "heatmap": 20, "heidelberg": 0, "heidelbergensi": 17, "height": [9, 11, 16, 19, 20], "hello": [16, 18, 20], "help": [16, 17], "henc": 16, "here": [15, 16, 17, 19, 20], "hex": 16, "hide": 20, "hierarch": [10, 11, 19, 20], "high": 19, "higher": 19, "highli": [16, 20], "highlight": [2, 16, 20], "hind": 20, "histori": 16, "hit": 16, "hls_to_rgb": 20, "hniavqylsefgdln": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeah": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqf": 15, "hniavqylsefgdlnealnsyyasqtddikdrreeahqfmaltnvshqfmaltnvsh": 15, "hniavqylsefgtddikdrreeah": 15, "hola": [16, 20], "hold": 19, "holt": 0, "home": [4, 11], "hominid": 15, "hominida": [17, 20], "hominina": 17, "hominoidea": 17, "homo": [15, 16, 17, 20], "homolog": 15, "hook": [16, 20], "hop": 11, "horizont": [9, 16], "host": [9, 11], "houben": 15, "hover": 16, "hoverenterev": 20, "hoverleaveev": 20, "how": [0, 4, 11, 15, 16, 18, 20], "howev": [1, 15, 17, 19, 20], "hsa": [15, 20], "hsa_001": 15, "hsa_002": 15, "hsa_003": 15, "hsa_004": 15, "html": [1, 9], "html_type": 9, "htmlface": 9, "http": [1, 11, 16, 17, 19], "hue": 20, "huerta": [0, 7, 15], "human": [7, 9, 11, 15, 19, 20], "human_1": 15, "human_2": 15, "human_3": 15, "human_orth": 9, "human_orth_prop": 9, "human_seq": 15, "humana": 15, "humanb": 15, "humanc": 15, "humand": 15, "humanfac": 20, "hundr": 15, "hz_line_color": [16, 20], "hz_line_typ": [16, 20], "hz_line_width": [9, 16, 20], "i": [0, 4, 5, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20], "id": [9, 11, 16, 19], "idea": [9, 11, 18, 19], "identifi": [7, 9, 15, 17], "idx": 9, "ignor": [15, 17], "ignore_unclassifi": [7, 10], "ikgskkaikvfssa": [16, 20], "imag": [11, 14, 16], "imagin": 18, "img": 9, "img_fac": 20, "img_path": [9, 20], "img_styl": [11, 20], "img_typ": 9, "imgfac": [9, 20], "implement": [1, 7, 19, 20], "import": [1, 5, 11, 15, 16, 17, 18, 19, 20], "impos": 18, "improv": [0, 15], "in_aligned_viewport": 9, "in_seq": [7, 15], "in_viewport": 9, "inch": [11, 20], "includ": [1, 5, 7, 8, 15, 16, 17, 18, 19, 20], "include_prop": [9, 11, 16], "include_root": 11, "inconsist": 5, "incorpor": 19, "incorrect": 18, "increas": 20, "inde": 19, "independ": [11, 16, 19, 20], "index": [2, 4, 5], "individu": 16, "infer": [7, 15, 17, 19], "info": [9, 11, 20], "inform": [7, 9, 11, 14, 16, 19, 20], "inherit": [9, 16], "init": 9, "init_from_et": 11, "init_from_newick": 11, "initi": [7, 9, 15, 16, 20], "initialize_tree_styl": 9, "inner": 19, "inner_bord": 20, "inparalog": 15, "input": [16, 17, 19], "insect": [19, 20], "insensit": 16, "insert": 5, "insert_intermedi": [3, 5], "insid": [16, 18], "instad": [7, 11], "instal": 20, "instanc": [1, 7, 10, 11, 15, 16, 17, 19, 20], "instantan": 19, "instead": [5, 11, 18, 19, 20], "int": [6, 9, 20], "intact": 19, "integ": 11, "integr": [16, 17, 20], "inter": 4, "interact": [11, 14], "interactiveitem": 20, "interchang": 5, "interchange_refer": [3, 5], "interclust": 4, "intercluster_dist": 4, "interest": [15, 19], "interfac": [16, 20], "interior": [5, 11], "interleav": [7, 8], "intermedi": [5, 11, 17], "intermediate_nod": [10, 17], "intern": [5, 7, 9, 10, 11, 15, 17, 19, 20], "internal_1": 19, "internal_2": 19, "internet": 17, "interpol": 16, "interpret": [4, 9, 11, 15, 16, 19], "interrupt": [16, 20], "intersect": 9, "intersects_angl": 9, "intersects_box": 9, "intersects_seg": 9, "intra": 4, "intraclust": 4, "intracluster_dist": 4, "intric": 19, "introduc": [16, 17], "introduct": 0, "invok": 20, "involv": [7, 15, 19], "iphylip": [7, 8, 15], "iphylip_relax": 8, "iphylip_txt": 15, "ipython": 16, "iq": 0, "is_collaps": 11, "is_fully_collaps": 9, "is_initi": 11, "is_leaf": [1, 6, 11, 16, 18, 19, 20], "is_leaf_fn": [5, 6, 7, 11, 19], "is_monophylet": 11, "is_root": [11, 16, 18, 19], "is_smal": 9, "is_vowel": 19, "issvsslllfnttenlykkyvfldplag": [16, 20], "item": [8, 9, 10, 11, 17, 19, 20], "itemfac": 20, "itep": 0, "iter": [5, 7, 8, 11, 18], "iter_entri": 8, "iter_prepostord": 11, "iter_speci": 7, "itertool": 11, "its": [0, 5, 6, 7, 9, 10, 11, 15, 16, 17, 19, 20], "itself": [11, 19], "j": [4, 7, 11, 18, 19], "jaim": 0, "jhcepa": [0, 11], "join": 15, "join_branch": [3, 5], "json": 9, "json_error": 9, "jupyt": 16, "just": [5, 11, 15, 18, 19], "k": [11, 18, 19], "kalinka": 15, "karg": [9, 20], "keep": [9, 10, 11, 15, 16, 19, 20], "keep_serv": [9, 11, 16], "kegg": 9, "kegg_enzym": 9, "kegg_modul": 9, "kegg_numb": 9, "kegg_pathwai": 9, "kei": [5, 7, 17, 19], "kept": [10, 11, 16, 17, 19, 20], "key_text": 9, "keyword": 12, "khaki": [16, 20], "kind": [9, 18, 19], "know": 18, "known": 20, "kwarg": [7, 8, 9], "l": [7, 15, 19, 20], "lab": 0, "label": [1, 7, 9, 15, 16, 17, 19, 20], "labl": 15, "ladder": [3, 5, 11], "laef": 20, "lai": 11, "lambda": [4, 11, 15, 17, 19], "larg": [9, 11, 16, 19], "larger": 19, "last": [5, 9, 11, 19], "later": [19, 20], "latest": [10, 17], "latter": 19, "launch": 11, "layout": [1, 11, 14, 15], "layout1": 9, "layout_alnface_compact": 16, "layout_alnface_grai": 16, "layout_barplot": 16, "layout_domain": 16, "layout_fn": [1, 20], "layout_heatmap": 16, "layout_seqfac": 16, "layout_tree_styl": 16, "layoutalign": 9, "layoutautonam": 9, "layoutbarplot": 9, "layoutbestnam": 9, "layoutbigg": 9, "layoutbranchlength": 9, "layoutbranchsupport": 9, "layoutcard": 9, "layoutcazi": 9, "layoutcuratednam": 9, "layoutetediffdist": 9, "layouteukog": 9, "layoutevolev": 9, "layoutgenomiccontext": 9, "layouthumanog": 9, "layoutkeggenzym": 9, "layoutkeggmodul": 9, "layoutkeggnumb": 9, "layoutkeggpathwai": 9, "layoutlastcommonancestor": 9, "layoutleafnam": 9, "layoutnumberleav": 9, "layoutoutlin": 9, "layoutpdb": 9, "layoutpfamdomain": 9, "layoutpreferrednam": 9, "layoutproteinnam": 9, "layoutscientificnam": 9, "layoutscinam": 9, "layoutse": 9, "layoutsmartdomain": 9, "layoutucsc": 9, "layoutucsctran": 9, "lca_fac": 16, "lead": 15, "leaf": [4, 5, 6, 7, 9, 10, 11, 15, 17, 18, 19], "leaf_nam": [11, 20], "leaf_profil": 4, "leaf_styl": 16, "leafnam": 7, "least": [16, 18], "leav": [1, 4, 5, 7, 9, 11, 15, 16, 17, 18, 20], "leaves_extra": 11, "leaves_onli": 11, "left": [9, 16, 19], "legend": 9, "legendfac": 9, "legibl": 18, "len": [18, 19, 20], "lenght": [5, 11, 19], "length": [1, 6, 9, 11, 15, 19], "less": [14, 19], "let": [15, 16, 18, 19, 20], "lett": 15, "letter": [5, 7, 11, 15], "level": [1, 5, 10, 11, 15, 16, 19], "levelord": [11, 12, 19], "lgqvpeidvpsylpdlpgiandlmyiadlgpgiapsapgtipelptfhtevaeplkvgelgsgmgagpgtp": [16, 20], "librari": 1, "licens": 16, "lightgrai": 9, "lightgreen": 20, "lightsteelblu": [16, 20], "like": [9, 11, 16, 17, 18, 19], "likelihood": 0, "limit": [6, 9, 15, 18, 19, 20], "linag": [7, 17], "line": [9, 11, 16, 19, 20], "line_typ": 9, "line_width": [9, 16], "lineag": [5, 7, 10, 11, 15, 17], "linear": 16, "link": [2, 4, 7, 14, 16, 19, 20], "link_to_align": [7, 15], "link_to_arrayt": 4, "linkag": 4, "linux": 0, "list": [0, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 20], "listen": [11, 16], "littl": 0, "load": [6, 9, 11, 15, 17, 19, 20], "load_tre": 9, "load_tree_from_newick": 9, "local": [7, 10, 14, 16, 18], "localhost": [9, 11, 16], "locat": [10, 19, 20], "long": [6, 16, 19, 20], "long_branch_nod": 19, "longer": [11, 20], "longest": 19, "longnamefac": 20, "look": [5, 18, 19], "lookup": 14, "loop": 19, "lose": 19, "loss": [7, 15], "lost": [5, 19], "lower": [16, 19], "lstrip": 16, "ltnvsh": 15, "ltnvshniavqylsefgdln": 15, "ltnvshqfma": 15, "luminos": 20, "lupu": 20, "m": 19, "m1_t1": 1, "m2_t1": 1, "m2_t2": 1, "m2_t3": 1, "m_1_t2": 1, "macaca": 15, "made": [16, 20], "madrid": 0, "maeapd": 15, "maeapdetiq": 15, "maeapdetiqqfm": 15, "maeapdetiqqfmaltnvshniavqylsefg": 15, "maeapdetiqqfmaltnvshniavqylsefgdln": 15, "maeipdatiq": 15, "maeipdatiqqfmaltnvshniavqi": 15, "maeipdetiq": 15, "maeipdetiqqfmalt": 15, "mai": [15, 19], "main": [1, 2, 3, 9, 16, 17, 18, 19, 20], "maintain": [0, 20], "mainten": 9, "major": 16, "make": [1, 5, 11, 16, 17, 18, 19, 20], "make_box": 9, "make_fac": 9, "make_nam": [3, 5, 9], "make_pars": 6, "maltnvshqfmaltnvsh": 15, "mammal": [15, 20], "mammalia": 17, "mani": [1, 7, 9, 11, 15, 19, 20], "manipul": [1, 16, 19, 20], "manual": 20, "map": [7, 11, 15, 16], "map_attribut": 11, "map_featur": 15, "map_prop": 11, "map_properti": 7, "marcet": [7, 15], "margin": 20, "margin_bottom": 20, "margin_left": 20, "margin_right": 20, "margin_top": 20, "mark": 9, "master": [19, 20], "master_li": 20, "masteritem": 20, "match": [3, 4, 7, 9, 10, 11, 12, 15, 18], "matcher": [2, 3, 14], "matches2": 19, "math": [4, 16], "matplotlib": 16, "matrix": 11, "max": [16, 20], "max_fsiz": [9, 16], "max_len": 6, "max_mb": 9, "max_rf": 19, "max_siz": 9, "max_tim": 9, "max_treeko_splits_to_be_artifact": 11, "maxcolor": 16, "maximum": [0, 8, 9, 19], "maxval": 16, "mean": [4, 15, 16, 20], "mechan": 11, "melanogast": [15, 20], "member": 20, "memori": [9, 10, 19], "mention": 19, "mesothorax": 20, "metagenom": 0, "metathorax": 20, "metazoa": [15, 17, 19], "method": [0, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "metric": 19, "microbi": 0, "middl": 5, "midpoint": [3, 5, 14], "millimet": [11, 20], "min": 10, "min_fsiz": [9, 16], "min_siz": [9, 16], "min_support_ref": 11, "min_support_sourc": 11, "min_support_t1": 11, "min_support_t2": 11, "min_x": 9, "mincolor": 16, "minim": [9, 10], "minimap": 16, "minimum": 11, "minimum_dr": 9, "minimum_dx": 9, "minnow": 20, "minval": 16, "miss": [15, 19], "mistak": 19, "mix": 16, "mixed_motif": [16, 20], "mm": [11, 15, 20], "mms_001": 15, "mmu": 15, "mmu_001": 15, "mmu_002": 15, "mmu_004": 15, "moccasin": [16, 20], "mode": [1, 20], "model": [5, 11], "modfii": 16, "modif": [5, 11, 20], "modifi": [1, 14, 16, 20], "modify_face_posit": 16, "modify_face_properti": 16, "modify_node_styl": 16, "modify_tree_styl": 16, "modtifi": 16, "modul": [2, 8, 9, 12, 16, 17, 18, 19, 20], "mol": 0, "molbev": 0, "molecular": [15, 16, 20], "moment": [19, 20], "monophylet": [10, 11, 19], "monophyli": [11, 14], "more": [1, 5, 7, 11, 15, 16, 18, 19, 20], "moreov": 19, "most": [15, 16, 17, 18, 19], "motif": [9, 16, 20], "mous": [15, 16, 20], "mousea": 15, "mousec": 15, "mousefac": 20, "move": [3, 5], "mpl": 16, "msa": [15, 16], "msa_layout": 16, "msdlfnklvmrrkgisgkgpgagdgpggafa": [16, 20], "msw046": 0, "mu": [15, 17, 20], "much": 15, "mulata": 15, "multifurc": [11, 14], "multilin": 20, "multipl": [2, 3, 7, 14, 17], "mundo": [16, 20], "musculu": [15, 17, 20], "must": [16, 19, 20], "my": [4, 11, 16, 20], "my_dist_fn": 4, "my_layout": 1, "my_tre": 1, "mylayout": 20, "mylegend": 16, "mynewick": 15, "mytre": [1, 20], "mytreefil": 1, "mytreelayout": 16, "n": [6, 8, 9, 11, 15, 16, 18, 19, 20], "n1": [5, 16, 19, 20], "n2": [5, 16, 19, 20], "n2content": 10, "n2leav": 18, "n3": [16, 20], "n4": [16, 20], "n_col": 9, "n_row": 9, "name": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 17, 18, 19], "name2seq": 16, "name2taxid": 17, "name_fac": 1, "name_newick": 9, "named_lineag": [7, 10, 17], "namedtupl": 9, "namefac": 20, "names_librari": 19, "namespac": 17, "natur": [0, 19], "navig": 19, "ncbi": [7, 10, 14], "ncbi_compar": 7, "ncbi_taxonomi": 17, "ncbitaxa": [3, 17], "nchildren": 18, "ndup": 15, "neanderthalensi": 17, "necessari": [5, 11, 15, 17, 19], "need": [1, 6, 9, 10, 12, 15, 16, 19, 20], "neg": 18, "nematod": 19, "nest": 19, "never": 19, "nevertheless": 19, "new": [5, 7, 9, 11, 15, 16, 18, 19], "new_tre": 19, "newick": [3, 4, 7, 9, 11, 12, 14, 15, 16, 17, 18], "newick_onli": [7, 15], "newickerror": 6, "newli": [5, 11], "next": [9, 11, 19, 20], "nexu": 3, "nexuserror": 6, "nhx": [6, 15, 19], "niavqi": 15, "niavqylsef": 15, "nice_html": 9, "nick": 17, "node": [4, 5, 6, 7, 9, 10, 11, 12, 14, 17], "node1": [5, 11, 19], "node2": [5, 11, 19], "node2label": 19, "node2leav": 19, "node3": 19, "node_background": [16, 20], "node_id": [5, 9, 11], "node_nam": 7, "node_name_str": 15, "node_s": 9, "node_styl": [11, 20], "node_style_default": 9, "nodecolor": 9, "nodecount": 16, "nodenam": 7, "nodes": 9, "nodes_text": 6, "nodestyl": [3, 16, 20], "nodestyle_differ": 16, "nodestyle_triangl": 16, "nodetyp": 19, "non": 15, "non_conserved_color": 9, "none": [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 18, 19, 20], "nopen": 20, "nor": 19, "norm_rf": 19, "normal": [9, 15, 17, 18, 19, 20], "notabl": 16, "notat": 19, "note": [1, 7, 11, 15, 16, 17, 18, 19, 20], "notebook": 16, "notic": 15, "noutahi": 0, "nov": 16, "novel": 16, "now": [15, 16, 18, 19, 20], "np": 16, "npanel": 9, "nsearch": 18, "nside": 9, "nst1": [16, 20], "nst2": [16, 20], "nst3": [16, 20], "nst4": [16, 20], "nstyle": 20, "ntree": 15, "number": [4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "numer": [16, 17], "numpi": [4, 16], "nw": [1, 4, 9, 11, 15, 16, 19, 20], "o": [11, 16, 19, 20], "o__korarchaeal": 17, "o__peptococcal": 17, "obj": 6, "object": [4, 6, 7, 9, 11, 19, 20], "obligatori": 16, "observ": 15, "obtain": [15, 19], "obvious": 19, "occupi": 16, "occur": 11, "occurr": 19, "ocur": 7, "offer": 17, "offici": 17, "often": [15, 18, 19], "og": 9, "ok": 19, "okai": 18, "old": [5, 11], "older": 15, "oldest": [7, 15], "on_first_visit": 9, "on_last_visit": 9, "onc": [15, 16, 17, 19, 20], "one": [1, 4, 7, 9, 11, 15, 16, 17, 18, 19, 20], "ones": 18, "onli": [1, 5, 7, 9, 11, 14, 15, 16, 17, 19, 20], "opac": [9, 16, 20], "open": [1, 4, 9, 10, 11, 16, 19], "open_brows": [9, 11], "open_browser_window": 9, "oper": [2, 3, 8, 11, 14, 20], "opisthokonta": 17, "opposit": 19, "optim": 11, "option": [1, 7, 12, 16, 18, 19, 20], "orang": [16, 20], "orangutan": 15, "order": [5, 11, 15, 16, 17, 19, 20], "ordercarnivora": 20, "orderless": 11, "org": [1, 11, 19], "organ": 17, "orient": 9, "origin": [0, 5, 7, 11, 15, 16, 17, 19, 20], "orphan": 19, "ortholog": 15, "orthologi": [0, 15], "other": [1, 5, 7, 11, 12, 15, 16, 17, 19, 20], "otherwis": [5, 10, 11, 15, 16], "our": [11, 15, 16, 18, 19, 20], "out_seq": [7, 15], "outfil": [7, 8, 11, 19], "outgroup": [5, 11, 14], "outlin": 9, "outline_color": 16, "outline_line_color": 16, "outline_line_width": 16, "outline_opac": 16, "outlinedfac": 16, "outlinefac": 9, "outparalog": 15, "output": [7, 8, 11, 15, 16, 18], "outsid": 14, "over": [1, 7, 8, 11, 15, 18, 19, 20], "overlap": [7, 16, 19], "overrid": 11, "overriden": 9, "overview": 14, "overwrit": 19, "overwriten": 15, "own": [1, 15, 16, 19, 20], "p": [4, 15, 16, 18, 19], "p1": 9, "p2": 9, "p__firmicutes_b": 17, "p__huberarchaeota": 17, "p__thermoproteota": 17, "packag": [1, 15, 17], "pad": [9, 11, 16], "padding_i": [9, 16], "padding_x": [9, 16], "page": [2, 15, 16, 20], "pair": [11, 15, 16, 20], "pan": [0, 15, 17, 20], "panel": 9, "para": 19, "paralog": 15, "paralogi": 15, "param": 7, "paramet": [4, 5, 7, 8, 9, 10, 11, 12, 16, 20], "paraphylet": 19, "parent": [5, 9, 10, 11, 16, 18, 19], "parent_child_t": 11, "parent_of": 9, "parenthes": 19, "parenthesi": 18, "pars": [0, 4, 7, 10, 11, 15, 17, 19], "parse_sp_nam": 7, "parser": [1, 2, 3, 4, 7, 9, 11, 12, 15, 18, 19], "part": [9, 15, 17, 18, 19, 20], "parti": 17, "partial": 19, "partit": [5, 7, 11, 15, 19], "parts_t1": 19, "parts_t2": 19, "pass": [11, 15, 16, 17, 18, 19, 20], "past": [11, 19], "path": [8, 11, 15, 19, 20], "pathogen": 0, "pathwai": 9, "pattern": [9, 12, 18, 19], "pda": [5, 11], "pdb": 9, "pdf": [11, 16, 20], "peer": 0, "per": [11, 15, 20], "perfect": 15, "perform": [9, 15, 16, 19, 20], "perman": 11, "permit": [16, 20], "permut": [11, 18], "pf": 16, "pfam": 9, "php": 11, "phy003i7zj_chick": 16, "phylemon": 0, "phylet": 19, "phylip": [7, 8], "phylip_relax": 8, "phylo": 15, "phylogenet": [0, 1, 2, 3, 5, 11, 14, 19], "phylogeni": [0, 15], "phylogenom": 0, "phylogent": 7, "phylom": 7, "phylomedb": 0, "phylosoft": 19, "phylostratigraf": 7, "phylotre": [3, 10, 15, 17, 18, 19], "phylum": 17, "pi": 9, "pickl": [9, 19], "pictur": 20, "piec": [9, 16, 20], "piechartfac": 9, "piexl": 16, "pile": [16, 20], "pink": [16, 20], "pixel": [9, 11, 16, 20], "place": [5, 11, 12, 15, 19, 20], "plai": 20, "plain": 19, "pleas": 11, "plot": [0, 20], "pname": 9, "png": [11, 20], "po": [6, 9], "point": [5, 9, 11, 15, 17, 19], "pointer": [7, 19, 20], "pointinghandcursor": 20, "polar": 19, "poli": 19, "polynod": 19, "polyphoni": 0, "polyphylet": 19, "polytomi": [5, 11, 19], "polytomy_size_limit": 11, "pop_child": 11, "popul": [1, 3, 5, 11, 16, 19, 20], "populate_uniform": [3, 5], "populate_yul": [3, 5], "popup": [9, 11], "port": [9, 11], "port_max": 9, "port_min": 9, "portal": 17, "portion": 19, "posibl": 11, "posit": [1, 5, 6, 11, 18, 19], "possess": 20, "possibl": [7, 9, 11, 15, 19, 20], "post": [1, 5, 9, 11, 19], "postord": [11, 19], "poswidth": [9, 16], "power": [16, 18], "pr_name": 11, "pr_valu": 11, "practic": 19, "pre": [1, 5, 10, 11, 16, 19, 20], "precis": 15, "precomput": 19, "predefin": [15, 20], "predict": 15, "prefer": [1, 9, 15], "prefix": 16, "preorder": [11, 19], "preprar": 17, "present": [0, 1, 7, 9, 10, 11, 15, 19], "preserve_branch_length": [11, 19], "prevent_nondicotom": 11, "previou": [15, 16, 18, 19], "previous": [9, 15, 19, 20], "primat": [15, 17, 19, 20], "print": [1, 5, 8, 11, 15, 16, 17, 18, 19], "print_frequnc": 16, "prior": 19, "probabl": 20, "process": [7, 9, 15, 17, 19], "processable_nod": 19, "produc": [0, 5, 11, 18, 19], "product": 0, "profil": [4, 20], "profilefac": 20, "program": [1, 16, 18, 19, 20], "programm": [15, 16, 20], "programmat": 0, "prop": [1, 5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "prop_nam": [11, 19], "prop_repr": 6, "prop_t1": 11, "prop_t2": 11, "proper": 19, "properti": [1, 4, 5, 6, 7, 9, 10, 11, 14, 15, 17], "proport": 20, "prot_nam": 9, "prota": 17, "protb": 17, "protc": 17, "protd": 17, "protein": [0, 9], "protocol": 11, "provid": [1, 7, 8, 9, 10, 11, 15, 16, 17, 19, 20], "proxi": 15, "prun": 5, "prune": [7, 9, 10, 11, 14, 15, 16, 17], "prune_by_select": 9, "ptr": [15, 20], "ptr_001": 15, "ptr_002": 15, "ptr_004": 15, "pure": 16, "purpl": [16, 19, 20], "purpos": 15, "put": [5, 9, 11, 16], "px": [11, 20], "px0": 11, "py": [11, 16, 20], "pyqt6": 20, "python": [0, 1, 11, 12, 15, 16, 18, 19, 20], "pyx": [4, 11], "q": 19, "qaggigkaklrsmkerklekqqqkeqeqvratsqgghl": [16, 20], "qbrush": 20, "qcolor": 20, "qfmalt": 15, "qfmaltnvsh": 15, "qgraphicsellipseitem": 20, "qgraphicsitem": 20, "qgraphicsrectitem": 20, "qgraphicssimpletextitem": 20, "qpen": 20, "qt": [2, 3, 14], "qtcore": 20, "qtgui": 20, "qtwidget": 20, "queri": [7, 16, 17, 19], "question": 2, "quickli": [1, 18, 19], "quiet": [9, 11, 16], "quit": [16, 18, 20], "quot": [6, 16, 18], "r": [0, 6, 9, 15, 16, 19], "r1": 19, "r109": 7, "r2": 19, "r3": 19, "r4": 19, "r5": 19, "r6": 19, "radiu": [9, 20], "rais": [5, 11, 19], "randint": [16, 20], "random": [5, 11, 16, 19, 20], "random_branch": [1, 16, 20], "random_color": 20, "randomli": [5, 7, 11], "rang": [9, 15, 16, 20], "rank": [7, 10, 17], "rank_limit": 10, "raster": 20, "rat": 15, "ratc": 15, "rate": 15, "rather": [11, 15, 17], "ratio": [16, 20], "re": [12, 18, 19, 20], "reach": 19, "read": [2, 6, 7, 9, 14, 15, 16, 20], "read_cont": 6, "read_nod": 6, "readi": 20, "real": [5, 11, 15, 20], "realat": 18, "realiti": 11, "realli": 19, "reason": [7, 11, 15, 18, 19], "receiv": [7, 11, 20], "recogn": 17, "recommend": [11, 19], "recomput": 11, "recon_tre": 15, "reconcil": [7, 15], "reconcili": 7, "reconstruct": 0, "recov": 15, "rect": [9, 20], "rect_fac": 16, "rect_typ": 9, "rect_width": 9, "rectangl": [9, 16], "rectangular": [9, 16, 20], "rectfac": [9, 16], "recurs": 19, "recycl": [16, 20], "red": [9, 16, 20], "reeah": 15, "reeahq": 15, "ref": [16, 20], "ref_edg": 19, "ref_edges_in_sourc": 19, "ref_tre": 11, "ref_tree_attr": 11, "refer": [2, 5, 7, 11, 15, 16, 17, 19, 20], "referenc": 9, "regard": [16, 19, 20], "regex": [16, 18], "regexp": 16, "region": 9, "regular": 18, "rehang": [3, 5], "rel": [7, 11, 14, 18], "relat": [2, 5, 11, 17, 18, 19], "relationship": [11, 15, 19], "relative_dist": 15, "relax": 8, "releas": 17, "reliabl": 19, "reload": 15, "remain": 19, "rememb": 17, "remov": [1, 3, 5, 9, 11], "remove_act": 9, "remove_active_clad": 9, "remove_child": [11, 19], "remove_children": 11, "remove_search": 9, "remove_select": 9, "remove_sist": 11, "removed_nod": 19, "render": [1, 3, 11, 14, 15, 16], "replic": 20, "report": [10, 17], "repr_short": 6, "repres": [4, 5, 6, 9, 10, 11, 15, 16, 17, 19, 20], "represent": [6, 7, 8, 9, 11, 16, 19, 20], "reproduc": [0, 11, 20], "reprophylo": 0, "req_json": 9, "request": [9, 11], "requir": [7, 10, 11, 15, 17, 18, 19, 20], "rerio": 20, "reset": 9, "resolut": [11, 20], "resolv": [5, 11], "resolve_polytomi": [3, 5, 11, 19], "resourc": [2, 17], "respect": [5, 19], "rest": [9, 19, 20], "restrict": 12, "result": [4, 5, 8, 9, 10, 11, 15, 18, 19], "retain": 11, "retriev": [9, 15, 17, 19], "retrieve_layout": 9, "retrieve_tree_data": 9, "return": [4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19, 20], "return_copi": 7, "return_tre": [10, 17], "revers": [5, 9, 11], "reverse_children": 11, "review": 19, "rf": [11, 19], "rf_max": [11, 19], "rgb": 20, "rgradient": [16, 20], "rhombu": 9, "rhombus_typ": 9, "rid": 10, "right": [1, 9, 11, 16, 19, 20], "rise": 15, "rmsd": 0, "robinson": 11, "robinson_fould": [11, 19], "rodent": 20, "rokubacterial": 16, "root": [5, 7, 11, 14, 16, 17, 18, 20], "root_at": [3, 5], "root_opening_factor": 20, "root_styl": 16, "rooted_tre": 19, "rotat": [9, 16], "rotate_text": 16, "rousseeuw": 4, "row": [4, 9, 11], "royalblu": 20, "rreeahqfma": 15, "rs_gcf_000019605": 17, "rs_gcf_001477695": 10, "rs_gcf_003948265": 17, "rstrip": 16, "rule": [16, 20], "run": [1, 16, 18], "run_smartview": 9, "rvsdsipplpppqqpqaed": [16, 20], "rx": 9, "ry": 9, "s1": 9, "s2": 9, "s__b65": 17, "s__jacael01": 17, "s__korarchaeum": 17, "s__mp8t": 17, "s__owc5": 17, "s__shmx01": 17, "s__smtz1": 17, "s__tekir": 17, "s__wtck01": 17, "safe": [9, 19], "safe_mod": 9, "safe_str": 9, "safer": [9, 12], "safer_ev": [3, 9, 12], "sai": 19, "same": [1, 7, 9, 11, 15, 16, 17, 18, 19, 20], "sametre": 15, "sampl": 17, "sample1": 16, "san": [9, 16], "sapien": [15, 17, 20], "sarcopterygii": 17, "satisfi": [12, 16], "satur": 20, "save": [1, 9, 15, 16, 19, 20], "scale": [7, 9, 15, 16], "scale_rang": [9, 16], "scalefac": [9, 16], "scan": [7, 15], "scheme": [16, 19], "sci_nam": [7, 9, 10, 11, 17], "scientif": [7, 9, 10, 17, 20], "scikit": 11, "scipi": 0, "score": [10, 15, 19], "scratch": 20, "script": [0, 1, 17], "se": 20, "search": [2, 3, 5, 9, 11, 12, 18], "search_ancestor": [11, 19], "search_by_s": 19, "search_descend": [11, 19], "search_leaves_by_nam": [11, 19], "search_nod": [11, 15, 19], "search_to_select": 9, "searched_bi": 9, "second": [9, 15, 18, 19], "section": [6, 16, 19], "section_nam": 6, "sector": 9, "see": [4, 7, 9, 11, 15, 16, 18, 19, 20], "seed": [9, 11], "seem": 18, "seen": [1, 7, 11, 19], "segment": 9, "select": [5, 9, 11, 19], "selected_children": 9, "selected_fac": 9, "selected_face_po": 9, "selectedcirclefac": 9, "selectedfac": 9, "selectedrectfac": 9, "self": [5, 7, 9, 11, 16, 19, 20], "semi": 20, "sensit": 16, "sent": [16, 20], "sep": 16, "separ": [15, 19], "seq": [7, 8, 16, 20], "seq1": 8, "seq2": 8, "seq_fac": 16, "seq_format": [9, 16, 20], "seq_motif_fac": 20, "seqa": 15, "seqb": 15, "seqc": 15, "seqd": 15, "seqfac": [9, 16, 20], "seqgroup": [2, 3, 15], "seqmotiffac": [9, 16, 20], "seqs_str": 8, "seqtyp": [9, 16], "sequenc": [2, 3, 5, 7, 9, 11, 14], "sequencefac": [16, 20], "sequenci": 8, "seri": [5, 9, 11], "serial": 19, "serialis": [11, 19], "serif": [9, 16], "serious": 19, "serra": 0, "serv": [11, 17], "server": [0, 3, 11, 16, 17], "session": [11, 18, 20], "set": [4, 5, 7, 8, 9, 10, 11, 14, 15, 16, 19, 20], "set_distance_funct": 4, "set_midpoint_outgroup": [3, 5], "set_node_styl": [9, 16], "set_outgroup": [3, 5, 11, 19], "set_seq": 8, "set_species_naming_funct": [7, 15], "set_styl": [11, 16, 20], "set_tree_styl": [9, 16], "setacceptshoverev": 20, "setbrush": 20, "setcursor": 20, "setparentitem": 20, "setpen": 20, "setpo": 20, "setrect": 20, "settext": 20, "setvis": 20, "setzvalu": 20, "sever": [0, 1, 11, 15, 16, 17, 18, 19, 20], "shape": [16, 20], "share": [11, 17, 19], "shell": 1, "shift": 5, "short": [5, 11, 18], "shortcut": [1, 16, 18], "should": [5, 7, 11, 12, 15, 16, 19, 20], "show": [1, 9, 11, 15, 19], "show_branch_length": [11, 16, 20], "show_branch_support": [11, 16, 20], "show_intern": [11, 15, 19], "show_leaf_nam": [1, 11, 16, 20], "shown": [9, 15, 16, 20], "sibl": 17, "side": [7, 11, 16], "signifi": 17, "signific": 19, "significantli": 15, "silhouet": 4, "silhouett": 4, "silouett": 4, "sim": 10, "simiiform": 17, "similar": [10, 12, 16, 17, 19], "similarli": [15, 19], "simpl": [1, 4, 14, 15, 17, 19, 20], "simple_motif": [16, 20], "simpler": 15, "simpli": [16, 20], "sinc": [11, 15, 17, 18, 19], "singl": [4, 7, 10, 11, 15, 16, 19, 20], "sister": [5, 11, 19], "site": 10, "size": [1, 5, 7, 9, 10, 11, 16, 19, 20], "size_prop": 9, "skbio_tre": 11, "skbiotre": 11, "skip": 17, "skip_large_polytomi": 11, "skip_quoted_nam": 6, "skip_spaces_and_com": 6, "skyblu": 16, "slice_typ": 9, "slightli": [1, 19], "slist": 15, "slowdown": 19, "slower": [11, 19], "slowest": [11, 19], "sm_style": [9, 11, 16], "small": [1, 16, 19, 20], "small_t": 20, "smaller": [16, 19], "smallest": 17, "smart": [9, 16], "smartview": [2, 3, 11, 16], "so": [1, 5, 7, 11, 16, 17, 18, 19], "socket": 9, "softwar": 19, "solid": [9, 16, 20], "solut": [11, 19], "solv": 14, "some": [9, 15, 16, 17, 19, 20], "someth": [12, 18], "sometim": [19, 20], "sort": [3, 5, 9, 10, 11, 20], "sort_descend": 11, "sos_thr": [7, 15], "sourc": [4, 6, 7, 8, 9, 10, 12, 16, 19, 20], "source_edg": 19, "source_edges_in_ref": 19, "source_subtre": 19, "source_tree_attr": 11, "sp": [16, 17], "sp001563325": 17, "sp001563335": 17, "sp001940705": 17, "sp002825465": 17, "sp002825515": 17, "sp002825535": 17, "sp002965065": 16, "sp003344655": 17, "sp003345545": 17, "sp003345555": 17, "sp003345595": 17, "sp003662765": 17, "sp004376265": 17, "sp004524435": 17, "sp004524445": 17, "sp004524565": 17, "sp004524595": 17, "sp005281345": 16, "sp008080745": 17, "sp011364905": 17, "sp011364985": 17, "sp011365025": 17, "sp013138615": 17, "sp013388835": 17, "sp020833055": 17, "sp_naming_funct": [7, 15, 17], "spain": 0, "span": 9, "sparingli": 18, "spci": 7, "spcode": [15, 17], "spearman_dist": 4, "speci": [0, 1, 7, 10, 11, 14, 16, 18, 19, 20], "special": [16, 18, 19, 20], "speciat": [7, 15, 19], "speciation_color": 9, "species2ag": [7, 15], "species_tre": 7, "species_tree_nw": 15, "specif": [7, 16, 17, 19, 20], "specifi": [1, 4, 9, 11, 15, 19], "speed": [11, 15], "sphere": 20, "split": [7, 17, 19], "split_by_dup": [7, 15], "split_thru_negative_xaxi": 9, "spname": 7, "spt": 15, "sptree": 15, "spx": 16, "sqlite": 17, "squar": [9, 16], "stack": 9, "stackedbarfac": 9, "stackoverflow": 0, "standalon": [1, 15], "standard": [7, 11, 19, 20], "start": [1, 5, 6, 9, 11, 16, 18, 19, 20], "startswith": [15, 16, 20], "state": 15, "statement": 19, "static": [11, 16, 20], "statist": 9, "statu": 9, "step": [5, 11, 17, 19], "still": [5, 11], "stolpii": 17, "store": [7, 8, 9, 11, 12, 15, 16, 17, 19], "store_act": 9, "store_search": 9, "store_select": 9, "str": [7, 9, 11], "straightforward": 16, "strain": 10, "strategi": [1, 11, 12, 17, 19], "streptomedb": 0, "streptomycet": 0, "strict": [15, 19], "strictli": [15, 19], "string": [1, 4, 7, 8, 10, 11, 12, 15, 19], "stroke_color": 9, "stroke_width": 9, "strongli": [12, 19], "structur": [0, 2, 4, 7, 11, 14, 15, 16, 18, 20], "studi": [7, 15], "style": [1, 9, 11, 14], "style1": 20, "style2": 20, "sub": [9, 10, 18, 19], "subclass": 9, "subfamili": 17, "subformat": 1, "submodul": 9, "subpart": [15, 19], "subset": 19, "subsp": 17, "subspeci": [10, 17, 20], "substitut": [5, 15, 18], "subtre": [7, 9, 12, 16, 18, 19, 20], "success": 19, "suit": [14, 16], "sum": [5, 11, 19], "summar": 9, "summari": 9, "summarize_inner_nod": 9, "sup": 18, "super": [16, 20], "superior": 19, "superkingdom": 17, "superord": 17, "supli": 11, "suppli": [7, 11], "support": [0, 5, 6, 8, 9, 11, 18, 19], "support_fn": [5, 11], "sure": 11, "svg": [11, 16, 20], "swap": 5, "swap_children": 11, "swap_prop": [3, 5], "symmetr": 11, "synonym": 15, "syntax": 19, "system": [10, 20], "t": [0, 1, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20], "t1": [1, 4, 11, 19], "t2": [1, 4, 11, 15, 19], "t3": [4, 11, 19], "t4": [4, 11], "tabl": [11, 16, 20], "tag": 19, "take": [7, 15, 17, 18, 19], "talk": 9, "tar": [10, 17], "targer": 16, "target": [11, 16, 19], "target2": 11, "task": [9, 19], "tax": 10, "tax2lineag": [7, 17], "tax2nam": [7, 10, 17], "tax2rank": [7, 10, 17], "tax2track": [7, 10, 17], "taxa": [10, 14], "taxa_lineag": 10, "taxdump": [10, 17], "taxdump_fil": 10, "taxid": [7, 9, 10, 14], "taxid2nam": 17, "taxid_attr": [7, 10, 17], "taxnam": 10, "taxon": 17, "taxonom": [14, 17], "taxonomi": [2, 3, 7, 14], "taxonomic_info": 15, "taxonomyi": 17, "techniqu": 19, "teleostomi": 17, "tell": 18, "tempor": [7, 15], "ten": 15, "tend": 16, "term": 19, "termin": [1, 11, 15, 16, 19, 20], "test": [0, 14], "tetrapoda": 17, "text": [6, 8, 9, 11, 15, 16, 17, 19, 20], "text_arrai": 4, "text_color": 9, "text_sect": 6, "text_typ": 9, "textcolor": 9, "textfac": [9, 16, 20], "th": 20, "than": [1, 5, 11, 15, 16, 17, 19, 20], "thats": 16, "thei": [6, 7, 11, 15, 16, 17, 19, 20], "them": [1, 5, 8, 11, 15, 16, 18, 19, 20], "themselv": [11, 19], "therefor": [15, 16, 19], "theria": 17, "theta": 11, "thi": [1, 4, 5, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20], "thing": [11, 18], "third": [17, 19], "those": [11, 15, 16], "thousand": 15, "three": [11, 15, 16, 18, 19], "threshold": [15, 16], "through": [15, 16, 17, 19, 20], "thu": [11, 15, 16, 19, 20], "thvmlgaeteeklfdaplsiskreqleqqvpenyfyvpd": [16, 20], "tick_width": [9, 16], "tid": 9, "time": [15, 17, 18, 19, 20], "timer": 9, "tip": [7, 9, 11, 18, 19], "tip1": 1, "titl": [9, 16], "tmp": 9, "tmsqfnfssapagggfsfstpkt": 16, "to_dendrogram": [3, 5], "to_hex": 16, "to_rgb": 16, "to_str": [11, 15, 17, 18, 19], "to_ultrametr": [1, 3, 5, 11], "togeth": [16, 19], "too": [5, 7, 11, 12, 19], "tool": [2, 19], "toolkit": [0, 17, 19, 20], "tooltip": [9, 16], "tooltip_prop": 9, "top": [9, 11, 16, 19, 20], "top_textfac": 16, "toplog": 19, "topmost": 19, "topolog": [5, 7, 11, 15, 18, 19], "topologi": [1, 5, 7, 11, 14, 15, 16, 20], "total": 19, "touch_and_get": 9, "tp": 18, "track": [7, 10, 17], "tran": 9, "transfer": [11, 19], "transform": 6, "translat": [6, 7, 10, 15, 17], "translate_to_nam": [10, 17], "transpar": [10, 16, 17, 20], "travers": [1, 3, 5, 11, 14, 18, 20], "traverse_bf": [3, 5], "tree": [0, 2, 3, 4, 6, 9, 10, 14], "tree1": 19, "tree2": 19, "tree_class": 6, "tree_data": 9, "tree_fac": 20, "tree_id": 9, "tree_layout": 16, "tree_styl": [1, 9, 11, 15, 16, 20], "tree_text": 6, "tree_width": 20, "treeactiv": 9, "treedata": 9, "treefac": 20, "treefil": 16, "treeko": [0, 7, 19], "treeko_dist": 19, "treelayout": 16, "treelayout_1": 16, "treematch": 18, "treenod": 11, "treepattern": [3, 12, 18], "treestyl": [1, 3, 11, 15, 16, 20], "treestyle_1": 16, "treestyle_legend": 16, "treeview": [2, 3, 20], "triangl": [9, 16], "triangle_node_styl": 16, "triangle_typ": 9, "trie": 0, "trig": 16, "trigger": 16, "tripl": 18, "troglodyt": [15, 17, 20], "tropic": 20, "true": [1, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 19, 20], "try": [9, 18], "try_synonym": 10, "ttttttttttttt": 8, "tupl": [8, 9, 11, 20], "tutori": [1, 2], "tutorial_tre": 1, "tw": 20, "two": [4, 5, 11, 15, 16, 18, 19, 20], "txt": 9, "type": [1, 9, 11, 15, 16, 19, 20], "typic": [5, 11], "u": [6, 16, 19, 20], "uba": 16, "uba2009": 16, "ucsc": 9, "ucsc_tran": 9, "ucsc_trans_prop": 9, "ugly_name_fac": 20, "ultrametr": [1, 5, 9, 11, 16], "unalign": 15, "unclassifi": 17, "uncommon": 19, "under": [0, 4, 10, 11, 15, 16, 19], "underscor": 15, "understand": [14, 16], "understood": [16, 19, 20], "unicod": 6, "uniform": [5, 11], "uniformli": 11, "uniqu": [7, 9, 11, 17], "unit": [0, 11, 20], "unless": 19, "unnecessari": 19, "unquot": 6, "unroot": [3, 5, 11], "unrooted_tre": [11, 19], "unselect_nod": 9, "until": 11, "up": [11, 14, 18, 19, 20], "updat": [5, 8, 9, 10, 11, 15, 17], "update_app_available_layout": 9, "update_layout": 9, "update_node_prop": 9, "update_node_styl": 9, "update_s": [3, 5], "update_select": 9, "update_sizes_al": [3, 5], "update_sizes_from": [3, 5], "update_taxonomy_databas": [10, 17], "upgrad": 16, "upper": [10, 19], "us": [2, 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 19, 20], "usag": 16, "use_collater": 11, "useless": 15, "user": [4, 11, 16, 17, 19, 20], "usual": [15, 17, 19], "util": [16, 17], "utterli": 9, "v": [0, 16, 20], "v0": 16, "v3": 16, "v4": [16, 17], "valencia": 0, "valid": [4, 5, 7, 9, 10, 11, 19], "valu": [4, 5, 7, 9, 11, 15, 16, 17, 18, 19, 20], "value_rang": [9, 16], "vari": 15, "variabl": [9, 14, 16], "variant": 18, "variat": 19, "variou": 16, "ve": 17, "vector": [1, 20], "veri": [16, 19, 20], "versa": 17, "version": [1, 7, 9, 12, 15, 17, 19], "vertebr": 15, "vertebrata": 17, "vertic": [9, 16], "verticl": 16, "vice": 17, "viceversa": 5, "view": [19, 20], "viewport": 9, "visit": [11, 19], "visual": [0, 2, 11, 14, 19], "vowel": [16, 19, 20], "vowel_color": 16, "vowel_node_layout": 16, "vowel_node_s": 16, "vowel_textfac": 16, "vowel_tree_styl": 16, "vqylsefgdlnealnsyyasqtddqpdrreeahqfmaltnvsh": 15, "vt_line_color": [16, 20], "vt_line_typ": [16, 20], "vt_line_width": [9, 16, 20], "w": [1, 11, 16, 19, 20], "wa": [0, 5, 6, 19, 20], "wai": [0, 1, 11, 15, 17, 18, 19, 20], "walk": [3, 5], "walker": [3, 5], "want": [1, 5, 11, 16, 18, 19, 20], "we": [5, 9, 11, 15, 16, 17, 18, 19, 20], "web": [0, 2, 3, 14, 17], "weight": 20, "well": [10, 15, 19], "were": 19, "werkmanii": 16, "what": [9, 12, 16, 18, 19], "whatev": 9, "when": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "where": [5, 6, 7, 9, 11, 15, 16, 17, 18, 19, 20], "whether": 16, "which": [7, 11, 15, 16, 17, 19, 20], "while": [15, 17, 20], "white": [16, 20], "whitespac": 6, "whole": [11, 15, 17, 19, 20], "whose": [5, 16, 19, 20], "wide": [7, 15, 19], "width": [9, 11, 16, 20], "win": 18, "window": 9, "wing": 20, "within": [7, 9, 11, 14, 15, 16, 17], "without": [11, 15, 19], "wolf": 20, "won": 11, "word": [0, 10, 15, 19], "work": [2, 7, 14, 20], "world": 9, "would": [9, 15, 18, 19], "wrap": 16, "write": [2, 7, 8, 11, 14, 15, 16, 18], "written": [8, 20], "wsgirefserv": 16, "www": 19, "x": [4, 6, 9, 11, 16, 18], "xor": 11, "xx": 18, "y": [4, 6, 9, 11, 16, 18, 19], "yasqtddikd": 15, "yasqtddqpd": 15, "yayqtddqkd": 15, "yayqtddqkdrreeahqfmaltnvsh": 15, "ye": [1, 15, 18], "yeast": [15, 19], "yeast_1": 15, "yeast_2": 15, "yellow": [16, 19, 20], "yield": [4, 5, 9, 11, 12, 18, 19], "you": [1, 7, 8, 15, 16, 17, 19, 20], "younga": 16, "youngblut": 17, "your": [1, 15, 16, 17, 19], "yqtddqkdrreeah": 15, "yule": [5, 11], "yyasqtddikdrreeah": 15, "z": 11, "za": 16, "zebrafish": 20, "zero": [11, 19], "zoom": [9, 16], "zvalu": 20, "zx": [9, 16], "zy": [9, 16]}, "titles": ["About", "Frequently Asked Questions", "Welcome to ETE\u2019s documentation!", "Reference Guide", "Clustering", "Tree operations", "Parsers", "Phylogenetic trees", "Multiple Sequence Alignments (SeqGroup)", "Smartview (web graphics)", "Taxonomy databases", "Tree (main class)", "Tree matcher", "Treeview (qt graphics)", "Tutorial", "Phylogenetic trees", "Tree drawing and exploration (web)", "Taxonomy databases", "Tree matcher", "Working with the Tree structure", "Tree drawing (Qt)"], "titleterms": {"": [2, 16, 19], "1": 16, "180": 20, "2": 16, "3": 16, "A": [15, 18], "The": 19, "about": 0, "ad": 15, "add": [16, 20], "advanc": [16, 19], "algorithm": 15, "align": [8, 15, 16], "all": [1, 19], "ancestor": 19, "annot": [1, 16, 17, 19], "ar": 1, "ask": 1, "aspect": [16, 20], "attribut": 19, "automat": [15, 17], "background": [16, 20], "bar": 16, "basic": 19, "between": [17, 19, 20], "branch": [1, 16, 19, 20], "brows": [1, 19], "bubbl": 20, "cach": 19, "can": 1, "chang": 20, "check": 19, "circular": [1, 20], "clade": 16, "class": 11, "closer": 15, "cluster": 4, "collaps": [15, 16, 19], "color": 16, "combin": [16, 20], "common": 19, "compar": 19, "concaten": 19, "content": [1, 2, 9, 13, 15, 16, 17, 18, 19, 20], "context": 9, "control": [1, 15, 16], "copi": [17, 19], "creat": [19, 20], "criteria": 19, "custom": [15, 16, 19, 20], "databas": [10, 17], "date": 15, "default": 9, "defin": 16, "degre": 20, "delet": 19, "descend": [17, 19], "detach": 19, "detect": 15, "differ": 17, "distanc": 19, "do": 1, "document": 2, "domain": [9, 16, 20], "download": 16, "draw": [1, 9, 16, 20], "drawer": 9, "duplic": [15, 19], "eggnog6": 9, "elimin": 19, "et": [0, 1, 2, 19], "ete4": 17, "etecompar": 9, "event": 15, "evocel": 9, "evol_ev": 9, "evolev": 7, "evolutionari": 15, "exampl": [16, 18], "explor": 16, "export": 1, "express": [16, 18], "face": [9, 13, 16, 20], "famili": 15, "faster": 19, "find": [1, 19], "first": 19, "fix": [16, 20], "format": 1, "fould": 19, "frequent": 1, "from": [18, 19], "function": [16, 19, 20], "gene": 15, "gener": 1, "get": [17, 19], "given": 19, "graphic": [9, 13], "gtdb": 17, "gtdbtaxa": 10, "guid": 3, "heatmap": 16, "helper": 9, "highlight": 0, "how": [1, 19], "i": 1, "imag": [1, 20], "img": 20, "implement": 15, "improv": 1, "indic": 2, "info": 15, "inform": [15, 17], "interact": [16, 20], "intern": 1, "iter": 19, "its": 1, "layout": [9, 16, 20], "leaf": [1, 16, 20], "leav": 19, "legend": [16, 20], "length": [16, 20], "less": 18, "link": [0, 15], "list": 19, "load": 1, "local": 17, "look": 15, "lookup": 19, "main": 11, "manual": 15, "map": 20, "match": [16, 19], "matcher": [12, 18], "mean": 19, "midpoint": 19, "mode": 16, "modifi": 19, "monophyli": 19, "multifurc": 19, "multipl": [8, 15, 16], "name": [1, 16, 20], "ncbi": 17, "ncbi_taxonomi": 9, "ncbitaxa": 10, "newick": [1, 6, 19], "nexu": 6, "node": [1, 15, 16, 18, 19, 20], "nodestyl": [9, 13], "object": [15, 16], "onli": 18, "oper": [5, 19], "order": 1, "outgroup": [15, 19], "outlin": 16, "outsid": 18, "overlap": 15, "overral": 16, "overview": [15, 16, 17, 20], "panel": 16, "parser": 6, "phylocloud_egg5": 9, "phylogenet": [7, 15, 20], "phylotre": 7, "plot": 16, "pop": 16, "posit": [9, 16, 20], "possibl": 16, "properti": [16, 19, 20], "prune": 19, "qt": [13, 20], "question": 1, "read": [1, 19], "reconcili": 15, "refer": 3, "regular": 16, "rel": [15, 19], "relat": 0, "remov": 19, "render": [9, 20], "resourc": 0, "robinson": 19, "root": [15, 19], "rotat": 20, "scale": 20, "scratch": 19, "script": 16, "search": [16, 19], "select": 16, "separ": 20, "seq": 9, "seqgroup": 8, "sequenc": [8, 15, 16, 20], "server": 9, "session": 16, "set": 17, "shortcut": 19, "show": [16, 20], "simpl": [16, 18], "smartview": 9, "so": 15, "solv": 19, "speci": [15, 17], "specif": 15, "split": 15, "spongilla": 9, "standalon": 16, "stapl": 9, "strip": 16, "structur": 19, "style": [16, 20], "suit": 18, "support": [1, 16, 20], "svg": 1, "tab": 16, "tabl": 2, "taxa": 17, "taxid": 17, "taxonom": 15, "taxonomi": [10, 17], "test": 18, "titl": 20, "tool": 0, "topolog": 16, "topologi": [17, 18, 19], "travers": 19, "tree": [1, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20], "treeko": 15, "treelayout": 9, "treestyl": [9, 13], "treeview": 13, "tutori": 14, "unbalanc": 1, "understand": 19, "unroot": 19, "up": [16, 17], "us": [0, 1, 17], "variabl": 18, "verbos": 16, "veri": 1, "visit": 1, "visual": [1, 15, 16, 20], "web": [9, 16], "welcom": 2, "which": 1, "while": 19, "within": [1, 19, 20], "work": [15, 19], "write": [1, 19], "x": 20, "y": 20, "your": 20, "zoom": 20}})
\ No newline at end of file
diff --git a/tutorial/tutorial_taxonomy.html b/tutorial/tutorial_taxonomy.html
index 8356d2fa..b3b8bd36 100644
--- a/tutorial/tutorial_taxonomy.html
+++ b/tutorial/tutorial_taxonomy.html
@@ -226,19 +226,7 @@ 
      GTDB taxonomy
 
 
      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.
      
+
      Give a list of GTDB string taxids, return a dictionary with their corresponding ranks.
      
 
 
      GTDBTaxa.get_name_lineage(taxnames)
      
 
      Given a valid taxname, return its corresponding lineage track as a hierarchically sorted list of parent taxnames.