skbio.tree.TreeNode#

class skbio.tree.TreeNode(name=None, length=None, support=None, parent=None, children=None)[source]#

Representation of a node within a tree.

A TreeNode instance stores links to its parent and optional children nodes. In addition, the TreeNode can represent a length (e.g., a branch length) between itself and its parent. Within this object, the use of “children” and “descendants” is frequent in the documentation. A child is a direct descendant of a node, while descendants are all nodes that are below a given node (e.g., grand-children, etc).

Parameters:
namestr or None

A node can have a name. It is common for tips in particular to have names, for instance, in a phylogenetic tree where the tips correspond to species.

lengthfloat, int, or None

Length of the branch connecting this node to its parent. Can represent ellapsed time, amount of mutations, or other measures of evolutionary distance.

supportfloat, int, or None

Support value of the branch connecting this node to its parent. Can be bootstrap value, posterior probability, or other metrics measuring the confidence or frequency of this branch.

parentTreeNode or None

Connect this node to a parent

childrenlist of TreeNode or None

Connect this node to existing children

Attributes

default_write_format

Built-ins

__copy__()

Return a copy of self using an iterative approach.

__deepcopy__()

Return a copy of self using an iterative approach.

__eq__(value, /)

Return self==value.

__ge__(value, /)

Return self>=value.

__getitem__(i)

Node delegates slicing to children.

__getstate__(/)

Helper for pickle.

__gt__(value, /)

Return self>value.

__hash__(/)

Return hash(self).

__iter__()

Node iter iterates over the children.

__le__(value, /)

Return self<=value.

__len__()

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.

__str__()

Return string version of self, with names and distances.

Methods

accumulate_to_ancestor(ancestor)

Return the sum of the distance between self and ancestor.

ancestors()

Return all ancestors back to the root.

append(node)

Append a node to children, in-place, cleaning up refs.

ascii_art([show_internal, compact])

Return a string containing an ascii drawing of the tree.

assign_ids()

Assign topologically stable unique ids to self.

assign_supports()

Extract support values from internal node labels of a tree.

bifurcate([insert_length])

Reorder the tree into a bifurcating tree.

cache_attr(func, cache_attrname[, cache_type])

Cache attributes on internal nodes of the tree.

compare_rfd(other[, proportion])

Calculate the Robinson and Foulds symmetric difference.

compare_subsets(other[, exclude_absent_taxa])

Return fraction of overlapping subsets where self and other differ.

compare_tip_distances(other[, sample, ...])

Compare self to other using tip-to-tip distance matrices.

copy()

Return a copy of self using an iterative approach.

count([tips])

Get the count of nodes in the tree.

create_caches()

Construct an internal lookups to facilitate searching by name.

deepcopy()

Return a copy of self using an iterative approach.

descending_branch_length([tip_subset])

Find total descending branch length from self or subset of self tips.

distance(other)

Return the distance between self and other.

extend(nodes)

Append a list of TreeNode to self.

find(name)

Find a node by name.

find_all(name)

Find all nodes that match name.

find_by_func(func)

Find all nodes given a function.

find_by_id(node_id)

Find a node by id.

from_linkage_matrix(linkage_matrix, id_list)

Return tree from SciPy linkage matrix.

from_taxdump(nodes[, names])

Construct a tree from the NCBI taxonomy database.

from_taxonomy(lineage_map)

Construct a tree from a taxonomy.

get_max_distance()

Return the max tip tip distance between any pair of tips.

has_children()

Return True if the node has children.

index_tree()

Index a tree for rapid lookups within a tree array.

invalidate_caches([attr])

Delete lookup and attribute caches.

is_root()

Return True if the current is a root, i.e. has no parent.

is_tip()

Return True if the current node has no children.

lca(tipnames)

Find lowest common ancestor for a list of tips.

levelorder([include_self])

Perform levelorder iteration over tree.

lowest_common_ancestor(tipnames)

Find lowest common ancestor for a list of tips.

neighbors([ignore])

Return all nodes that are connected to self.

non_tips([include_self])

Iterate over nontips descended from self.

observed_node_counts(tip_counts)

Return counts of node observations from counts of tip observations.

pop([index])

Remove a TreeNode from self.

postorder([include_self])

Perform postorder iteration over tree.

pre_and_postorder([include_self])

Perform iteration over tree, visiting node before and after.

preorder([include_self])

Perform preorder iteration over tree.

prune()

Reconstruct correct topology after nodes have been removed.

read(file[, format])

Create a new TreeNode instance from a file.

remove(node)

Remove a node from self.

remove_deleted(func)

Delete nodes in which func(node) evaluates True.

root()

Return root of the tree which contains self.

root_at(node)

Return a new tree rooted at the provided node.

root_at_midpoint()

Return a new tree rooted at midpoint of the two tips farthest apart.

shear(names)

Remove tips until the tree just has the desired tip names.

shuffle([k, names, shuffle_f, n])

Yield trees with shuffled tip names.

siblings()

Return all nodes that are children of self parent.

subset()

Return set of names that descend from specified node.

subsets()

Return all sets of names that come from self and its descendants.

subtree([tip_list])

Make a copy of the subtree.

tip_tip_distances([endpoints])

Return distance matrix between pairs of tips, and a tip order.

tips([include_self])

Iterate over tips descended from self.

to_array([attrs, nan_length_value])

Return an array representation of self.

to_taxonomy([allow_empty, filter_f])

Return a taxonomy representation of self.

traverse([self_before, self_after, include_self])

Return iterator over descendants.

unpack()

Unpack an internal node in place.

unpack_by_func(func)

Unpack internal nodes of a tree that meet certain criteria.

unrooted_copy([parent])

Walk the tree unrooted-style and returns a copy.

unrooted_deepcopy([parent])

Walk the tree unrooted-style and returns a new copy.

write(file[, format])

Write an instance of TreeNode to a file.