historydag.from_newick

historydag.from_newick(tree, label_features, label_functions={}, newick_format=8, attr_func=lambda n: ...)[source]

Make a history DAG using a newick string. Internally, utilizes newick parsing features provided by ete3, then calls from_tree() on the resulting ete3.Tree object.

Parameters:

  • tree (str) – newick string representation of a tree. May contain extended node data in ‘extended newick format’ used by ete3.

  • label_features (List[str]) – (passed to from_tree()) list of features to be used as label fields in resulting history DAG. ‘name’ refers to the node name string in the standard newick format. See ete3 docs for more details.

  • newick_format – ete3 format number of passed newick string. See ete3 docs for details.

  • label_functions (Mapping[str, Callable[[TreeNode], Any]]) – (passed to from_tree())

  • attr_func (Callable[[TreeNode], Any]) – (passed to from_tree())

Return type:

HistoryDag

Returns:

HistoryDag object, which has the same topology as the input newick tree, with the required UA node added as a new root.