Package Bio :: Package Phylo :: Module TreeConstruction :: Class ParsimonyScorer
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Class ParsimonyScorer

source code

object --+    
         |    
    Scorer --+
             |
            ParsimonyScorer

Parsimony scorer with a scoring matrix.

This is a combination of Fitch algorithm and Sankoff algorithm. See ParsimonyTreeConstructor for usage.

Instance Methods [hide private]
 
__init__(self, matrix=None)
x.__init__(...) initializes x; see help(type(x)) for signature
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get_score(self, tree, alignment)
Calculate and return the parsimony score given a tree and the MSA using the Fitch algorithm without the penalty matrix the Sankoff algorithm with the matrix
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, matrix=None)
(Constructor)

source code 
x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • matrix, _Matrix - scoring matrix used in parsimony score calculation.
Overrides: object.__init__
(inherited documentation)

get_score(self, tree, alignment)

source code 
Calculate and return the parsimony score given a tree and the MSA using the Fitch algorithm without the penalty matrix the Sankoff algorithm with the matrix
Overrides: Scorer.get_score