Bio.Phylo.TreeConstruction.DistanceTreeConstructor

Trees Indices Help Biopython Package Bio :: Package Phylo :: Module TreeConstruction :: Class DistanceTreeConstructor [hide private] [frames] | no frames ] Class DistanceTreeConstructor source code object --+ | TreeConstructor --+ | DistanceTreeConstructor Distance based tree constructor. Examples Loading a small PHYLIP alignment from which to compute distances, and then build a upgma Tree: from Bio.Phylo.TreeConstruction import DistanceTreeConstructor from Bio.Phylo.TreeConstruction import DistanceCalculator from Bio import AlignIO aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip') constructor = DistanceTreeConstructor() calculator = DistanceCalculator('identity') dm = calculator.get_distance(aln) upgmatree = constructor.upgma(dm) print(upgmatree) Output: Tree(rooted=True) Clade(branch_length=0, name='Inner4') Clade(branch_length=0.18749999999999994, name='Inner1') Clade(branch_length=0.07692307692307693, name='Epsilon') Clade(branch_length=0.07692307692307693, name='Delta') Clade(branch_length=0.11057692307692304, name='Inner3') Clade(branch_length=0.038461538461538464, name='Inner2') Clade(branch_length=0.11538461538461536, name='Gamma')

Clade(branch_length=0.11538461538461536, name='Beta') Clade(branch_length=0.15384615384615383, name='Alpha') Build a NJ Tree: njtree = constructor.nj(dm) print(njtree) Output: Tree(rooted=False) Clade(branch_length=0, name='Inner3') Clade(branch_length=0.18269230769230765, name='Alpha') Clade(branch_length=0.04807692307692307, name='Beta') Clade(branch_length=0.04807692307692307, name='Inner2') Clade(branch_length=0.27884615384615385, name='Inner1') Clade(branch_length=0.051282051282051266, name='Epsilon') Clade(branch_length=0.10256410256410259, name='Delta') Clade(branch_length=0.14423076923076922, name='Gamma') Instance Methods __init__(self, source code distance_calc ulator=None, method='nj ') Initialize the class. build_tree(sel source code f, msa) Construct and return a Tree, Neighbor Joining or UPGMA. upgma(self, source code distance_mat rix) Construct and return an UPGMA tree.

nj(self, source code distance_mat rix) Construct and return a Neighbor Joining tree. _height_of(se source code [hide private] lf, clade) Calculate clade height -- the longest path to any terminal (PRIVATE). Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__ Class Variables [hide private] methods = ['nj', 'upgma'] Properties [hide private] Inherited from object: __class__ Method Details __init__(self, distance_calculator=None, method='nj') (Constructor) [hide private] source code Initialize the class.

Parameters: method (str) - Distance tree construction method, 'nj'(default) or 'upgma'. distance_calculator (DistanceCalculator) - The distance matrix calculator for multiple sequence alignment. It must be provided if build_tree will be called. Overrides: object.__init__ build_tree(self, msa) source code Construct and return a Tree, Neighbor Joining or UPGMA. Overrides: TreeConstructor.build_tree upgma(self, distance_matrix) source code Construct and return an UPGMA tree. Constructs and returns an Unweighted Pair Group Method with Arithmetic mean (UPGMA) tree. Parameters: distance_matrix (DistanceMatrix) - The distance matrix for tree construction. nj(self, distance_matrix) source code Construct and return a Neighbor Joining tree. Parameters: distance_matrix (DistanceMatrix) - The distance matrix for tree construction. Trees Indices Help Biopython Generated by Epydoc 3.0.1 on Wed Nov 6 13:32:28 2019 http://epydoc.sourceforge.net

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