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src/b/i/biopython-HEAD/Tests/test_TreeConstruction.py   biopython(Download)
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
from Bio.Phylo.TreeConstruction import ParsimonyScorer
from Bio.Phylo.TreeConstruction import NNITreeSearcher
from Bio.Phylo.TreeConstruction import ParsimonyTreeConstructor
 
        matrix = _Matrix(alphabet, step_matrix)
        scorer = ParsimonyScorer(matrix)
        searcher = NNITreeSearcher(scorer)
        trees = searcher._get_neighbors(tree)
        self.assertEqual(len(trees), 2 * (5 - 3))
        matrix = _Matrix(alphabet, step_matrix)
        scorer = ParsimonyScorer(matrix)
        searcher = NNITreeSearcher(scorer)
        constructor = ParsimonyTreeConstructor(searcher, tree1)
        best_tree = constructor.build_tree(aln)