cogent3.core.tree.PhyloNode

class PhyloNode(name: str, children: Iterable[Self | str] | None = None, parent: Self | None = None, params: dict[str, Any] | None = None, name_loaded: bool = True, length: float | None = None, support: float | None = None)

Store information about a tree node. Mutable.

Parameters:

name: label for the node, assumed to be unique. children: list of the node’s children. parent: parent to this node params: dict containing arbitrary parameters for the node. name_loaded: ?

Attributes:

children

length

name

name_loaded

params

parent

parent of this node

source

support

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, name_unnamed])	Wrap multifurcating with a num of 2
child_parent_map()	return dict of {<child name>: <parent name>, ...}
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_name(other)	Compares PhyloNode by name
copy([memo])	Returns a copy of self using an iterative approach
deepcopy([memo])	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_edge_names(tip_name_1, tip_name_2[, ...])	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_matching_name(name)	find the edge with the name
get_node_names([include_self, tips_only])	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_root()	Returns root of the tree self is in.
get_sub_tree(names[, ignore_missing, ...])	A new instance of a sub tree that contains all the otus that are listed in name_list.
get_tip_names([include_self])	return the list of the names of all tips contained by this edge
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
iter_tips([include_self])	Iterates over tips descended from self, [] if self is a tip.
ladderise()	Return an equivalent tree nodes using a ladderise sort.
ladderize()	Return an equivalent tree nodes using a ladderise sort.
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(tip_names)	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, name_unnamed])	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([keep_root, params_merge_callback])	removes nodes with one child
reassign_names(mapping[, nodes])	Reassigns node names based on a mapping dict
remove(target)	Removes node by name instead of identity.
remove_deleted(should_delete)	Removes all nodes where should_delete tests true.
remove_node(target)	Removes node by identity instead of value.
renamed_nodes(name_map)	returns a copy of the tree with nodes renamed according to name_map
root_at_midpoint()	return a new tree rooted at midpoint of the two tips farthest apart
rooted(edge_name)	Returns a new tree with split at edge_name
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.
separation(other)	Returns number of edges separating self and other.
set_param_value(param, edge, value)	set's the value for param at named edge
siblings()	Returns all nodes that are children of the same parent as self.
sorted([sort_order])	An equivalent tree with tips in sort_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_root_distances([names, ...])	returns the cumulative sum of lengths from each tip to the root
tip_to_tip_distances([names, 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
tree_distance(other[, method])	Return the specified tree distance between this and another tree.
unrooted()	A tree with at least 3 children at the root.
unrooted_deepcopy([parent])	Returns a deepcopy of the tree using unrooted traversal.
write(filename[, with_distances, format_name])	Save the tree to filename

get_neighbours_except
parse_token