phylox.parser

Functions

dinetwork_to_extended_newick(network[, simple])

Converts a phylogenetic network to a Newick string.

extended_newick_to_dinetwork(newick[, ...])

Converts a Newick string to a networkx DAG with leaf labels.
phylox.parser.dinetwork_to_extended_newick(network, simple=False)

Converts a phylogenetic network to a Newick string. The newick string has :length:bootstrap:probability annotations if any edge has a bootstrap or probability. If only lengths are available, the newick string has :length annotations.

Parameters:

  • network – a phylogenetic network, i.e., a phylox DiNetwork.

  • simple – Boolean, indicating whether to create a simple newick string without parameters

Returns:

a string in extended Newick format for phylogenetic networks.

Example:

>>> from phylox import DiNetwork
>>> from phylox.constants import LENGTH_ATTR
>>> from phylox.parser import dinetwork_to_extended_newick
>>> network = DiNetwork(
...     edges=[
...         (0, 1, {LENGTH_ATTR: 1.0}),
...         (0, 2, {LENGTH_ATTR: 1.0}),
...         (1, 3, {LENGTH_ATTR: 1.0}),
...         (2, 3, {LENGTH_ATTR: 1.0}),
...         (1, 4, {LENGTH_ATTR: 1.0}),
...         (2, 5, {LENGTH_ATTR: 1.0}),
...         (3, 6, {LENGTH_ATTR: 1.0}),
...     ],
...     labels=((0, "A"), (4, "B"), (5, "C"), (6, "D"), (3, "E")),
... )
>>> newick = dinetwork_to_extended_newick(network)
>>> "C:1.0" in newick
True
phylox.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