biopython

v1.71.0

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.

:Parameters:

matrix : _Matrix
    scoring matrix used in parsimony score calculation.

Link to this section Summary

Functions

__init__()

Initialize the class

get_score()

Calculate parsimony score using the Fitch algorithm

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function get_score()

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).