biopython v1.71.0 Bio.Phylo.TreeConstruction.ParsimonyScorer
Parsimony scorer with a scoring matrix.
This is a combination of Fitch algorithm and Sankoff algorithm. See ParsimonyTreeConstructor for usage.
matrix : _Matrix scoring matrix used in parsimony score calculation.
Link to this section Summary
Link to this section Functions
Initialize the class.
Calculate parsimony score using the Fitch algorithm
Calculate and return the parsimony score given a tree and the MSA using either the Fitch algorithm (without a penalty matrix) or the Sankoff algorithm (with a matrix).