biotite.sequence.phylo.Tree¶

class
biotite.sequence.phylo.
Tree
(root)¶ Bases:
biotite.copyable.Copyable
A Tree represents a rooted tree (e.g. alignment guide 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
).The amount of leaves in a tree can be determined via the len() function.
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
 rootTreeNode
The root node of the tree.
 leaveslist 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
(self)¶ 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
 newickstr
The Newick notation to create the tree from.
 labelslist 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
 treeTree
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 intermediate nodes. If the string contains such labels, they are discarded.

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, index2int
The reference indices of the two leaf nodes, to calculate the distance for.
 topologicalbool, optional
If True the topological distance is measured, i.e. all childparent distance is 1. Otherwise, the distances from the distance attribute are used.
 Returns
 distancefloat
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
 labelsiterable object of str
The labels the indices in the leaf nodes srefer to
 include_distancebool
If true, the distances are displayed in the newick notation, otherwise they are omitted.
 Returns
 newickstr
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);