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src/b/i/biopython-HEAD/Tests/test_TreeConstruction.py   biopython(Download)
from Bio.Phylo import TreeConstruction
from Bio.Phylo import Consensus
from Bio.Phylo.TreeConstruction import _Matrix
from Bio.Phylo.TreeConstruction import _DistanceMatrix
from Bio.Phylo.TreeConstruction import DistanceCalculator
                       [2.5,   1,    0],
                       [  1, 2.5,  2.5, 0]]
        matrix = _Matrix(alphabet, step_matrix)
        scorer = ParsimonyScorer(matrix)
        score = scorer.get_score(tree, aln)
                       [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0]]
 
        matrix = _Matrix(alphabet, step_matrix)
        scorer = ParsimonyScorer(matrix)
        score = scorer.get_score(tree, aln)
                       [2.5,   1,    0],
                       [  1, 2.5,  2.5, 0]]
        matrix = _Matrix(alphabet, step_matrix)
        scorer = ParsimonyScorer(matrix)
        searcher = NNITreeSearcher(scorer)
                       [2.5,   1,    0],
                       [  1, 2.5,  2.5, 0]]
        matrix = _Matrix(alphabet, step_matrix)
        scorer = ParsimonyScorer(matrix)
        searcher = NNITreeSearcher(scorer)