Package Bio :: Package Phylo :: Module PhyloXML :: Class Phylogeny
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Class Phylogeny

source code

          object --+        
                   |        
BaseTree.TreeElement --+    
                       |    
            PhyloElement --+
                           |
          object --+       |
                   |       |
BaseTree.TreeElement --+   |
                       |   |
          object --+   |   |
                   |   |   |
  BaseTree.TreeMixin --+   |
                       |   |
           BaseTree.Tree --+
                           |
                          Phylogeny

A phylogenetic tree.
Instance Methods [hide private]
 
__init__(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
as_phyloxml(self)
Return this tree, a PhyloXML-compatible Phylogeny object.
source code
 
to_phyloxml_container(self, **kwargs)
Create a new Phyloxml object containing just this phylogeny.
source code
 
to_alignment(self)
Construct an alignment from the aligned sequences in this tree.
source code
 
_get_confidence(self)
Equivalent to self.confidences[0] if there is only 1 value.
source code
 
_set_confidence(self, value) source code
 
_del_confidence(self) source code

Inherited from BaseTree.Tree: __format__, __str__, format, is_terminal, root_at_midpoint, root_with_outgroup

Inherited from BaseTree.TreeElement: __repr__

Inherited from BaseTree.TreeMixin: collapse, collapse_all, common_ancestor, count_terminals, depths, distance, find_any, find_clades, find_elements, get_nonterminals, get_path, get_terminals, is_bifurcating, is_monophyletic, is_parent_of, is_preterminal, ladderize, prune, split, total_branch_length, trace

Inherited from BaseTree.TreeMixin (private): _filter_search

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Class Methods [hide private]
 
from_tree(cls, tree, **kwargs)
Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).
source code
 
from_clade(cls, clade, **kwargs)
Create a new Phylogeny given a Newick or BaseTree Clade object.
source code

Inherited from BaseTree.Tree: randomized

Properties [hide private]
  confidence
Equivalent to self.confidences[0] if there is only 1 value.

Inherited from BaseTree.Tree: clade

Inherited from object: __class__

Method Details [hide private]

__init__(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None)
(Constructor)

source code 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Parameters:
  • root (Clade) - the root node/clade of this tree
  • rooted (bool) - True if this tree is rooted
  • rerootable (bool) - True if this tree is rerootable
  • branch_length_unit (string) - unit for branch_length values on clades
  • name (string) - identifier for this tree, not required to be unique
  • id (Id) - unique identifier for this tree
  • description (string) - plain-text description
  • date (Date) - date for the root node of this tree
  • confidences (list) - Confidence objects for this tree
  • clade_relations (list) - CladeRelation objects
  • sequence_relations (list) - SequenceRelation objects
  • properties (list) - Property objects
  • other (list) - non-phyloXML elements (type Other)
Overrides: object.__init__
(inherited documentation)

from_tree(cls, tree, **kwargs)
Class Method

source code 

Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).

Keyword arguments are the usual Phylogeny constructor parameters.

from_clade(cls, clade, **kwargs)
Class Method

source code 

Create a new Phylogeny given a Newick or BaseTree Clade object.

Keyword arguments are the usual PhyloXML.Clade constructor parameters.

Overrides: BaseTree.Tree.from_clade

as_phyloxml(self)

source code 

Return this tree, a PhyloXML-compatible Phylogeny object.

Overrides the BaseTree method.

Overrides: BaseTree.Tree.as_phyloxml

_get_confidence(self)

source code 

Equivalent to self.confidences[0] if there is only 1 value.

See also: Clade.confidence, Clade.taxonomy


Property Details [hide private]

confidence

Equivalent to self.confidences[0] if there is only 1 value.

See also: Clade.confidence, Clade.taxonomy

Get Method:
_get_confidence(self) - Equivalent to self.confidences[0] if there is only 1 value.
Set Method:
_set_confidence(self, value)
Delete Method:
_del_confidence(self)