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.

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_at_midpoint(self)
Root the tree at the midpoint of the two most distant taxa.

source code

root_with_outgroup(self, outgroup_targets, *more_targets, **kwargs)
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.

Parameters:

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

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.

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.

Parameters:

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_at_midpoint(self)

source code

Root the tree at the midpoint of the two most distant taxa.

This operates in-place, leaving a bifurcating root. The topology of the tree is otherwise retained, though no guarantees are made about the stability of clade/node/taxon ordering.

root_with_outgroup(self, outgroup_targets, *more_targets, **kwargs)

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

Parameters:

outgroup_branch_length - length of the branch leading to the outgroup after rerooting. If not specified (None), then:
- If the outgroup is an internal node (not a single terminal taxon), then use that node as the new root.
- Otherwise, create a new root node as the parent of the outgroup.

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_at_midpoint(self)

root_with_outgroup(self, outgroup_targets, *more_targets, **kwargs)

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