Tree Construction Tools

Classes and methods for tree construction.

class DistanceMatrix(names, matrix=None)

Distance matrix class that can be used for distance based tree algorithms.

All diagonal elements will be zero no matter what the users provide.

Initialize the class.

format_phylip(handle)

Write data in Phylip format to a given file-like object or handle.

The output stream is the input distance matrix format used with Phylip programs (e.g. ‘neighbor’). See: http://evolution.genetics.washington.edu/phylip/doc/neighbor.html

Parameters:

handle : file or file-like object

A writeable file handle or other object supporting the ‘write’ method, such as StringIO or sys.stdout. On Python 3, should be open in text mode.

class TreeConstructor

Base class for all tree constructor.

build_tree(msa)

Caller to built the tree from a MultipleSeqAlignment object.

This should be implemented in subclass.

class DistanceTreeConstructor(method='nj')

Distance based tree constructor.

Parameters:

method : str

Distance tree construction method, ‘nj’(default) or ‘upgma’.

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')

Initialize the class.

nj(distance_matrix)

Construct and return a Neighbor Joining tree.

Parameters:

distance_matrix : DistanceMatrix

The distance matrix for tree construction.

upgma(distance_matrix)

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.