prosstt.tree_utils module

This module contains utility functions for the Tree class.

prosstt.tree_utils.parse_newick(newick_tree, def_time)

Function that translates a Newick tree to a prosstt Tree object.

Parameters:

• newick_tree (Newick tree) – A Newick tree object as returned by the loads function of the newick package
• def_time (int) – The default pseudotime length of each tree branch

Returns:

• topology (list) – A list of connected branch names
• time (dict) – Contains the pseudotime length of each branch
• branches (list) – The name of each branch
• branch_points (int) – The number of branch points in the lineage tree
• root (str) – The name of the root of the lineage tree