build_tree_nj

build_tree_nj(population: Sequence[Union[HereditaryStratigraphicColumn, HereditaryStratigraphicSpecimen]], estimator: str, prior: str | Any, taxon_labels: Iterable | None = None, force_common_ancestry: bool = False, negative_origin_time_correction_method: str | None = None) → DataFrame

Estimate the phylogenetic history among hereditary stratigraphic columns by using the “unweighted pair group method with neighbor joinint distance-based reconstruction method.

This phylogenetic reconstruction approach is generally unfavorable, incuring O(n^2) runtime complexity and providing reconstructions that occasionally conflict with the hereditary stratigraphic record.

Parameters

population: Sequence[HereditaryStratigraphicArtifact]

Hereditary stratigraphic columns corresponding to extant population members.

Each member of population will correspond to a unique leaf node in the reconstructed tree.

estimator{“maximum_likelihood”, “unbiased”}

What estimation method should be used? Options are “maximum_likelihood” or “unbiased”.

See estimate_ranks_since_mrca_with for discussion of estimator options.

prior{“arbitrary”, “uniform”} or object implementing prior interface

Prior probability density distribution over possible generations of the MRCA.

See estimate_rank_of_mrca_between for discussion of prior options.

taxon_labels: Optional[Iterable], optional

How should leaf nodes representing extant hereditary stratigraphic columns be named?

Label order should correspond to the order of corresponding hereditary stratigraphic columns within population. If None, taxons will be named according to their numerical index.

force_common_ancestry: bool, default False

How should columns that definitively share no common ancestry be handled?

If set to True, treat columns with no common ancestry as if they shared a common ancestor immediately before the genesis of the lineages. If set to False, columns within population that definitively do not share common ancestry will raise a ValueError.

negative_origin_time_correction_method

: {“truncate”, “shift”, “rescale”}, optional How should negative origin time estimates be corrected?

Returns

pd.DataFrame

The reconstructed phylogenetic tree in alife standard format.