cassiopeia.tl.score_small_parsimony#
- cassiopeia.tl.score_small_parsimony(cassiopeia_tree, meta_item, root=None, infer_ancestral_states=True, label_key='label')[source]#
Computes the small-parsimony of the tree.
Using the meta data stored in the specified cell meta column, compute the parsimony score of the tree.
- Parameters:
- cassiopeia_tree
CassiopeiaTree CassiopeiaTree object with cell meta data.
- meta_item
str A column in the CassiopeiaTree cell meta corresponding to a categorical variable.
- root
str|NoneOptional[str] (default:None) Node to treat as the root. Only the subtree below this node will be considered.
- infer_ancestral_states
bool(default:True) Whether or not ancestral states must be inferred (this will be False if fitch_hartigan has already been called on the tree.)
- label_key
str|NoneOptional[str] (default:'label') If ancestral states have already been inferred, this key indicates the name of the attribute they’re stored in.
- cassiopeia_tree
- Return type:
- Returns:
The parsimony score.
- Raises:
CassiopeiaError if label_key has not been populated. –