PhyloTree

class PhyloTree(tree, tree_format='newick', copy=False)

Main class responsible for working with phylogenetic trees.

Constructor for PhyloTree.

Parameters

• tree (Union[str, _io.StringIO, pmaf.phylo.tree._metakit.PhyloTreeMetabase, ete3.coretype.tree.TreeNode]) – Tree data can be string, IO stream, any tree class from module ete3

• tree_format (str) – If tree is string-like then tree_format should be tree format

• copy (bool) – if tree is PhyloTree or any tree class from module ete3, then should copy made prior to construction or not.

Attributes

internal_node_names	List of internal node names.
internal_nodes	List of internal node instances.
node_names	List of all node names.
nodes	List of all nodes.
tip_names	List of all tip names.
tips	List of all tips.
total_internal_nodes	Total number of internal nodes.
total_nodes	Total number of nodes.
total_tips	Total number of tips.

Methods

annotate_nodes_by_map(node_mapping[, only_tips])	Annotate nodes by inserting annotation text based on node_mapping
clear_internal_node_names()	Delete internal node names.
copy()	Create a copy of self.
get_ascii_art()	Get ASCII tree art.
get_mcra_for_nodes(node_names)	Get MRCA node for the given list of node names.
get_newick_str(**kwargs)	Get Newick string of the tree.
get_node_by_name(node_name)	Get node instance by its name.
ladderize()	Sort branches of the tree from shortest to longest.
merge_nodes(tip_names)	Merge given tips into single node.
prune_by_ids(node_ids)	Prune the tree and keep the nodes/tips in node_ids
remove_node(node)	Delete the node.
remove_node_by_name(node_name)	Delete nodes by name
render(output_fp)	Render tree to the file.
replace_nodes_by_map(node_mapping[, only_tips])	Replace node names by map node_mapping
resolve_polytomy()	Resolve all polytomies and create a dicotomic tree structure.
sort_by_name()	Sort tips by names.
to_skbio([rooted])	Convert tree to skbioTreeNode
unroot()	Unroot the tree.
write(tree_fp, **kwargs)	Write tree to file.