alifestd_from_newick

alifestd_from_newick(newick: str, *, branch_length_dtype: type = <class 'float'>, create_ancestor_list: bool = False, dtype_id: type | None = <class 'numpy.int64'>) → DataFrame

Convert a Newick format string to a phylogeny dataframe.

Parses a Newick tree string and returns a pandas DataFrame in alife standard format with columns: id, ancestor_id, taxon_label, origin_time_delta, and branch_length. Optionally includes ancestor_list.

Parameters

newickstr

A phylogeny in Newick format.

branch_length_dtypetype, default float

Dtype for branch length values. Use int to get nullable integer columns (pd.Int64Dtype). Missing branch lengths will be pd.NA for integer dtypes or NaN for float dtypes.

create_ancestor_listbool, default False

If True, include an ancestor_list column in the result.

dtype_idtype or None, default np.int64

Numpy dtype for the id and ancestor_id columns. If None, the smallest signed integer dtype is chosen automatically based on the number of commas in the Newick string.

Returns

pd.DataFrame

Phylogeny dataframe in alife standard format.

See Also

alifestd_from_newick_polars :

Polars-based implementation.

alifestd_as_newick_asexual :

Inverse conversion, from alife standard to Newick format.