cogent3.core.tree.PhyloNode#

class PhyloNode(*args, **kwargs)#
Attributes
length
parent

Accessor for parent.

Methods

ancestors()

Returns all ancestors back to the root.

append(i)

Appends i to self.children, in-place, cleaning up refs.

ascii_art([show_internal, compact])

Returns a string containing an ascii drawing of the tree.

balanced()

Tree 'rooted' here with no neighbour having > 50% of the edges.

bifurcating([eps, constructor, name_unnamed])

Wrap multifurcating with a num of 2

child_groups()

Returns list containing lists of children sharing a state.

compare_by_names(other)

Equality test for trees by name

compare_by_subsets(other[, exclude_absent_taxa])

Returns fraction of overlapping subsets where self and other differ.

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

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

compare_name(other)

Compares TreeNode by name

copy([memo, _nil, constructor])

Returns a copy of self using an iterative approach

copy_topology([constructor])

Copies only the topology and labels of a tree, not any extra data.

deepcopy([memo, _nil, constructor])

Returns a copy of self using an iterative approach

descendant_array([tip_list])

Returns numpy array with nodes in rows and descendants in columns.

distance(other)

Returns branch length between self and other.

extend(items)

Extends self.children by items, in-place, cleaning up refs.

get_connecting_edges(name1, name2)

returns a list of edges connecting two nodes.

get_connecting_node(name1, name2)

Finds the last common ancestor of the two named edges.

get_distances([endpoints])

The distance matrix as a dictionary.

get_edge_names(tip1name, tip2name[, clade, ...])

Return the list of stem and/or sub tree (clade) edge name(s).

get_edge_vector([include_root])

Collect the list of edges in postfix order

get_figure([style])

gets Dendrogram for plotting the phylogeny

get_max_tip_tip_distance()

Returns the max tip-to-tip distance between any pair of tips

get_newick([with_distances, semicolon, ...])

Return the newick string of node and its descendents

get_node_names([includeself, tipsonly])

Return a list of edges from this edge - may or may not include self.

get_nodes_dict()

Returns a dict keyed by node name, value is node

get_param_value(param, edge)

returns the parameter value for named edge

get_sub_tree(name_list[, ignore_missing, ...])

A new instance of a sub tree that contains all the otus that are listed in name_list.

get_tip_names([includeself])

return the list of the names of all tips contained by this edge

get_xml()

Return XML formatted tree string.

index_in_parent()

Returns index of self in parent.

insert(index, i)

Inserts an item at specified position in self.children.

is_root()

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

is_tip()

Returns True if the current node is a tip, i.e. has no children.

isroot()

Returns True if root of a tree, i.e. no parent.

istip()

Returns True if is tip, i.e. no children.

iter_nontips([include_self])

Iterates over nontips descended from self, [] if none.

iter_tips([include_self])

Iterates over tips descended from self, [] if self is a tip.

last_common_ancestor(other)

Finds last common ancestor of self and other, or None.

lca(other)

Finds last common ancestor of self and other, or None.

levelorder([include_self])

Performs levelorder iteration over tree

lin_rajan_moret(tree2)

return the lin-rajan-moret distance between trees

lowest_common_ancestor(tipnames)

Lowest common ancestor for a list of tipnames

make_tree_array([dec_list])

Makes an array with nodes in rows and descendants in columns.

max_tip_tip_distance()

returns the max distance between any pair of tips

multifurcating(num[, eps, constructor, ...])

return a new tree with every node having num or few children

name_unnamed_nodes()

sets the Data property of unnamed nodes to an arbitrary value

non_tip_children()

Returns direct children in self that have descendants.

nontips([include_self])

Returns nontips descended from self.

pop([index])

Returns and deletes child of self at index (default: -1)

postorder([include_self])

performs postorder iteration over tree.

pre_and_postorder([include_self])

Performs iteration over tree, visiting node before and after.

preorder([include_self])

Performs preorder iteration over tree.

prune()

Reconstructs correct tree after nodes have been removed.

reassign_names(mapping[, nodes])

Reassigns node names based on a mapping dict

remove(target)

Removes node by name instead of identity.

remove_deleted(is_deleted)

Removes all nodes where is_deleted tests true.

remove_node(target)

Removes node by identity instead of value.

root()

Returns root of the tree self is in.

root_at_midpoint()

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

rooted_at(edge_name)

Return a new tree rooted at the provided node.

rooted_with_tip(outgroup_name)

A new tree with the named tip as one of the root's children

same_shape(other)

Ignores lengths and order, so trees should be sorted first

same_topology(other)

Tests whether two trees have the same topology.

scale_branch_lengths([max_length, ultrametric])

Scales BranchLengths in place to integers for ascii output.

separation(other)

Returns number of edges separating self and other.

set_max_tip_tip_distance()

Propagate tip distance information up the tree

set_param_value(param, edge, value)

set's the value for param at named edge

set_tip_distances()

Sets distance from each node to the most distant tip.

siblings()

Returns all nodes that are children of the same parent as self.

sorted([sort_order])

An equivalent tree sorted into a standard order.

subset()

Returns set of names that descend from specified node

subsets()

Returns all sets of names that come from specified node and its kids

tip_children()

Returns direct children of self that are tips.

tip_to_tip_distances([endpoints, default_length])

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

tips([include_self])

Returns tips descended from self, [] if self is a tip.

tips_within_distance(distance)

Returns tips within specified distance from self

to_json()

returns json formatted string {'newick': with edges and distances, 'edge_attributes': }

to_rich_dict()

returns {'newick': with node names, 'edge_attributes': {'tip1': {'length': ...}, ...}}

total_descending_branch_length()

Returns total descending branch length from self

total_length()

returns the sum of all branch lengths in tree

traverse([self_before, self_after, include_self])

Returns iterator over descendants.

unrooted()

A tree with at least 3 children at the root.

write(filename[, with_distances, format])

Save the tree to filename

get_node_matching_name

unrooted_deepcopy