Perform a BFS or DFS traversal through all elements in this tree.

:returns: generator of all elements for which filter_func is True.

Deletes target from the tree, relinking its children to its parent.

:returns: the parent clade.

Collapse all the descendents of this tree, leaving only terminals.

Total branch lengths are preserved, i.e. the distance to each terminal stays the same.

For example, this will safely collapse nodes with poor bootstrap support:

     >>> from Bio import Phylo
     >>> tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml')
     >>> print("Total branch length %0.2f" % tree.total_branch_length())
     Total branch length 20.44
     >>> tree.collapse_all(lambda c: c.confidence is not None and c.confidence < 70)
     >>> print("Total branch length %0.2f" % tree.total_branch_length())
     Total branch length 21.37

This implementation avoids strange side-effects by using level-order traversal and testing all clade properties (versus the target specification) up front. In particular, if a clade meets the target specification in the original tree, it will be collapsed. For example, if the condition is:

     >>> from Bio import Phylo
     >>> tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml')
     >>> print("Total branch length %0.2f" % tree.total_branch_length())
     Total branch length 20.44
     >>> tree.collapse_all(lambda c: c.branch_length < 0.1)
     >>> print("Total branch length %0.2f" % tree.total_branch_length())
     Total branch length 21.13

Collapsing a clade’s parent node adds the parent’s branch length to the child, so during the execution of collapse_all, a clade’s branch_length may increase. In this implementation, clades are collapsed according to their properties in the original tree, not the properties when tree traversal reaches the clade. (It’s easier to debug.) If you want the other behavior (incremental testing), modifying the source code of this function is straightforward.

Most recent common ancestor (clade) of all the given targets.

Edge cases:

• If no target is given, returns self.root
• If 1 target is given, returns the target
• If any target is not found in this tree, raises a ValueError

Counts the number of terminal (leaf) nodes within this tree.

Create a mapping of tree clades to depths (by branch length).

:Parameters:

unit_branch_lengths : bool
    If True, count only the number of branches (levels in the tree).
    By default the distance is the cumulative branch length leading
    to the clade.

:returns: dict of {clade: depth}, where keys are all of the Clade

instances in the tree, and values are the distance from the root to
each clade (including terminals).

Calculate the sum of the branch lengths between two targets.

If only one target is specified, the other is the root of this tree.

Return the first element found by find_elements(), or None.

This is also useful for checking whether any matching element exists in the tree, and can be used in a conditional expression.

Find each clade containing a matching element.

That is, find each element as with find_elements(), but return the corresponding clade object. (This is usually what you want.)

:returns: an iterable through all matching objects, searching

depth-first (preorder) by default.

Find all tree elements matching the given attributes.

The arbitrary keyword arguments indicate the attribute name of the sub-element and the value to match: string, integer or boolean. Strings are evaluated as regular expression matches; integers are compared directly for equality, and booleans evaluate the attribute’s truth value (True or False) before comparing. To handle nonzero floats, search with a boolean argument, then filter the result manually.

If no keyword arguments are given, then just the class type is used for matching.

The result is an iterable through all matching objects, by depth-first search. (Not necessarily the same order as the elements appear in the source file!)

:Parameters:

target : TreeElement instance, type, dict, or callable
    Specifies the characteristics to search for. (The default,
    TreeElement, matches any standard Bio.Phylo type.)
terminal : bool
    A boolean value to select for or against terminal nodes (a.k.a.
    leaf nodes). True searches for only terminal nodes, False
    excludes terminal nodes, and the default, None, searches both
    terminal and non-terminal nodes, as well as any tree elements
    lacking the ``is_terminal`` method.
order : {'preorder', 'postorder', 'level'}
    Tree traversal order: 'preorder' (default) is depth-first
    search, 'postorder' is DFS with child nodes preceding parents,
    and 'level' is breadth-first search.

Example

 >>> from Bio import Phylo
 >>> phx = Phylo.PhyloXMLIO.read('PhyloXML/phyloxml_examples.xml')
 >>> matches = phx.phylogenies[5].find_elements(code='OCTVU')
 >>> next(matches)
 Taxonomy(code='OCTVU', scientific_name='Octopus vulgaris')

Get a list of all of this tree’s nonterminal (internal) nodes.

List the clades directly between this root and the given target.

:returns: list of all clade objects along this path, ending with the

given target, but excluding the root clade.

Get a list of all of this tree’s terminal (leaf) nodes.

Return True if tree downstream of node is strictly bifurcating.

I.e., all nodes have either 2 or 0 children (internal or external, respectively). The root may have 3 descendents and still be considered part of a bifurcating tree, because it has no ancestor.

MRCA of terminals if they comprise a complete subclade, or False.

I.e., there exists a clade such that its terminals are the same set as the given targets.

The given targets must be terminals of the tree.

To match both Bio.Nexus.Trees and the other multi-target methods in Bio.Phylo, arguments to this method can be specified either of two ways: (i) as a single list of targets, or (ii) separately specified targets, e.g. is_monophyletic(t1, t2, t3) — but not both.

For convenience, this method returns the common ancestor (MCRA) of the targets if they are monophyletic (instead of the value True), and False otherwise.

:returns: common ancestor if terminals are monophyletic, otherwise False.

True if target is a descendent of this tree.

Not required to be a direct descendent.

To check only direct descendents of a clade, simply use list membership testing: if subclade in clade: ...

True if all direct descendents are terminal.

Sort clades in-place according to the number of terminal nodes.

Deepest clades are last by default. Use reverse=True to sort clades deepest-to-shallowest.

Prunes a terminal clade from the tree.

If taxon is from a bifurcation, the connecting node will be collapsed and its branch length added to remaining terminal node. This might be no longer be a meaningful value.

:returns: parent clade of the pruned target

Generate n (default 2) new descendants.

In a species tree, this is a speciation event.

New clades have the given branch_length and the same name as this clade’s root plus an integer suffix (counting from 0). For example, splitting a clade named “A” produces sub-clades named “A0” and “A1”. If the clade has no name, the prefix “n” is used for child nodes, e.g. “n0” and “n1”.

Calculate the sum of all the branch lengths in this tree.

List of all clade object between two targets in this tree.

Excluding start, including finish.