biotite.sequence.phylo.Tree¶

class
biotite.sequence.phylo.
Tree
(root)¶ Bases:
biotite.copyable.Copyable
A Tree represents a rooted binary tree (e.g. phylogentic tree). The tree itself is represented by TreeNode objects. The root node is accessible via the root property. The property leaves contains a list of the leaf nodes, where the index of the leaf node in this list is equal to the reference index of the leaf node (
leaf.index
).Two Tree objects are equal if they are the same object, so the
==
operator is equal to theis
operator.Objects of this class are immutable.
Parameters:  root: TreeNode
The root of the tree. The constructor calls the node’s as_root() method, in order to make it immutable.
Examples
>>> leaf1 = TreeNode(index=0) >>> leaf2 = TreeNode(index=1) >>> leaf3 = TreeNode(index=2) >>> inter = TreeNode(leaf1, leaf2, 5.0, 7.0) >>> root = TreeNode(inter, leaf3, 3.0, 10.0) >>> tree = Tree(root) >>> print(tree) ((0:5.0,1:7.0):3.0,2:10.0):0.0;
Attributes:  root : TreeNode
The root node of the tree.
 leaves : list of TreeNode
The leaf nodes of the tree. The index of the leaf node in this list is equal to the reference index of the leaf node. This attribute is a shallow copy of the repsective internal object.

copy
()¶ Create a deep copy of this object.
Returns:  copy
A copy of this object.

from_newick
(newick, labels=None)¶ Create a tree from a Newick notation.
Parameters:  newick : str
The Newick notation to create the tree from.
 labels : list of str, optional
If the Newick notation contains labels, that are not parseable into reference indices, i.e. they are not integers, this parameter can be provided to convert these labels into reference indices. The corresponding index is the position of the label in the provided list.
Returns:  tree : Tree
A tree created from the Newick notation
Notes
This function does accept but does not require the Newick string to have the terminal semicolon. Keep in mind that the Tree class does support any labels on intermeiate nodes. If the string contains such labels, they are discarded. Furthermore, only binary trees can be parsed.

get_distance
(index1, index2, topological=False)¶ Get the distance between two leaf nodes.
The distance is the sum of all distances from the each of the two nodes to their lowest common ancestor.
Parameters:  index1, index2
The reference indices of the two leaf nodes, to calculate the distance for.
Returns:  distance : float
The distance between the nodes.
Examples
>>> leaf1 = TreeNode(index=0) >>> leaf2 = TreeNode(index=1) >>> leaf3 = TreeNode(index=2) >>> inter = TreeNode(leaf1, leaf2, 5.0, 7.0) >>> root = TreeNode(inter, leaf3, 3.0, 10.0) >>> tree = Tree(root) >>> print(tree.get_distance(0,1)) 12.0 >>> print(tree.get_distance(0,2)) 18.0 >>> print(tree.get_distance(1,2)) 20.0

to_newick
(labels=None, include_distance=True)¶ Obtain the Newick notation of the tree.
Parameters:  labels : iterable object of str
The labels the indices in the leaf nodes srefer to
 include_distance : bool
If true, the distances are displayed in the newick notation, otherwise they are omitted.
Returns:  newick : str
The Newick notation of the tree.
Examples
>>> leaf1 = TreeNode(index=0) >>> leaf2 = TreeNode(index=1) >>> leaf3 = TreeNode(index=2) >>> inter = TreeNode(leaf1, leaf2, 5.0, 7.0) >>> root = TreeNode(inter, leaf3, 3.0, 10.0) >>> tree = Tree(root) >>> print(tree.to_newick()) ((0:5.0,1:7.0):3.0,2:10.0):0.0; >>> print(tree.to_newick(include_distance=False)) ((0,1),2); >>> labels = ["foo", "bar", "foobar"] >>> print(tree.to_newick(labels=labels, include_distance=False)) ((foo,bar),foobar);