Package Bio :: Package Phylo :: Module BaseTree :: Class Tree

Class Tree

 object --+    
          |    
TreeElement --+
              |
 object --+   |
          |   |
  TreeMixin --+
              |
             Tree

Known Subclasses:

A phylogenetic tree, containing global info for the phylogeny.

The structure and node-specific data is accessible through the 'root'
clade attached to the Tree instance.

:Parameters:
    root : Clade
        The starting node of the tree. If the tree is rooted, this will
        usually be the root node.
    rooted : bool
        Whether or not the tree is rooted. By default, a tree is assumed to
        be rooted.
    id : str
        The identifier of the tree, if there is one.
    name : str
        The name of the tree, in essence a label.

Instance Methods

[hide private]

__format__(self, format_spec)
Serialize the tree as a string in the specified file format.

source code

__init__(self, root=None, rooted=True, id=None, name=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

__str__(self)
String representation of the entire tree.

source code

as_phyloxml(self, **kwargs)
Convert this tree to a PhyloXML-compatible Phylogeny.

source code

format(self, format)
Serialize the tree as a string in the specified file format.

source code

is_terminal(self)
True if the root of this tree is terminal.

source code

root_with_outgroup(self, outgroup_targets, *more_targets)
Reroot this tree with the outgroup clade containing outgroup_targets.

source code

Inherited from TreeElement: __repr__

Inherited from 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 TreeMixin (private): _filter_search

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

Class Methods

[hide private]

from_clade(cls, clade, **kwargs)
Create a new Tree object given a clade.

source code

randomized(cls, taxa, branch_length=1.0, branch_stdev=None)
Create a randomized bifurcating tree given a list of taxa.

source code

Properties

[hide private]

clade
The first clade in this tree (not itself).

Inherited from object: __class__

Method Details

[hide private]

format(self, format_spec)

source code

Serialize the tree as a string in the specified file format.

This method supports the ``format`` built-in function added in Python
2.6/3.0.

:param format_spec: a lower-case string supported by `Bio.Phylo.write`
    as an output file format.

init(self, root=None, rooted=True, id=None, name=None)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

source code

String representation of the entire tree.

Serializes each sub-clade recursively using ``repr`` to create a summary
of the object structure.

Overrides: object.__str__

as_phyloxml(self, **kwargs)

source code

Convert this tree to a PhyloXML-compatible Phylogeny.

This lets you use the additional annotation types PhyloXML defines, and
save this information when you write this tree as 'phyloxml'.

format(self, format)

source code

Serialize the tree as a string in the specified file format.

This duplicates the __format__ magic method for pre-2.6 Pythons.

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

source code

Create a new Tree object given a clade.

Keyword arguments are the usual `Tree` constructor parameters.

randomized(cls, taxa, branch_length=1.0, branch_stdev=None)
Class Method

source code

Create a randomized bifurcating tree given a list of taxa.

:param taxa: Either an integer specifying the number of taxa to create
    (automatically named taxon#), or an iterable of taxon names, as
    strings.

:returns: a tree of the same type as this class.

root_with_outgroup(self, outgroup_targets, *more_targets)

source code

Reroot this tree with the outgroup clade containing outgroup_targets.

Operates in-place.

Edge cases:

- If ``outgroup == self.root``, no change
- If outgroup is terminal, create new bifurcating root node with a
  0-length branch to the outgroup
- If outgroup is internal, use the given outgroup node as the new
  trifurcating root, keeping branches the same
- If the original root was bifurcating, drop it from the tree,
  preserving total branch lengths

Property Details

[hide private]

clade

The first clade in this tree (not itself).

Get Method:: unreachable.clade(self) - The first clade in this tree (not itself).

Class Tree

__format__(self, format_spec)

__init__(self, root=None, rooted=True, id=None, name=None) (Constructor)

__str__(self) (Informal representation operator)

as_phyloxml(self, **kwargs)

format(self, format)

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

randomized(cls, taxa, branch_length=1.0, branch_stdev=None) Class Method

root_with_outgroup(self, outgroup_targets, *more_targets)

clade

format(self, format_spec)

init(self, root=None, rooted=True, id=None, name=None)
(Constructor)

str(self)
(Informal representation operator)

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

randomized(cls, taxa, branch_length=1.0, branch_stdev=None)
Class Method