phylox.newick_parser.extended_newick_to_dinetwork

phylox.newick_parser.extended_newick_to_dinetwork(newick, internal_labels=False)

Converts a Newick string to a networkx DAG with leaf labels. The newick string may or may not have length:bootstrap:probability annotations. The newick string may or may not have internal node labels. The newick string may or may not have hybrid nodes.

Parameters:

newick – a string in extended Newick format for phylogenetic networks.
internal_labels – a boolean, indicating whether the internal nodes of the network are labeled.

Returns:

a phylogenetic network, i.e., a networkx digraph with leaf labels represented by the `label’ node attribute.

Example:

>>> newick = "(A:1.1,B:1.2,(C:1.3,D:1.4)E:1.6)F;"
>>> network = extended_newick_to_dinetwork(newick)
>>> {network.nodes[leaf].get("label") for leaf in network.leaves} == {'A', 'B', 'C', 'D'}
True
>>> node_for_label_A = network.label_to_node_dict['A']
>>> p = network.parent(node_for_label_A)
>>> network[p][node_for_label_A]['length']
1.1