biopython

v1.71.0

biopython v1.71.0 Bio.Phylo.TreeConstruction.DistanceTreeConstructor

Distance based tree constructor.

: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.

Example

 >>> from TreeConstruction import DistanceTreeConstructor
 >>> constructor = DistanceTreeConstructor()

UPGMA Tree:

 >>> upgmatree = constructor.upgma(dm)
 >>> print upgmatree
 Tree(rooted=True)
     Clade(name='Inner4')
         Clade(branch_length=0.171955155115, name='Inner1')
             Clade(branch_length=0.111111111111, name='Epsilon')
             Clade(branch_length=0.111111111111, name='Delta')
         Clade(branch_length=0.0673103855608, name='Inner3')
             Clade(branch_length=0.0907558806655, name='Inner2')
                 Clade(branch_length=0.125, name='Gamma')
                 Clade(branch_length=0.125, name='Beta')
             Clade(branch_length=0.215755880666, name='Alpha')

NJ Tree:

 >>> njtree = constructor.nj(dm)
 >>> print njtree
 Tree(rooted=False)
     Clade(name='Inner3')
         Clade(branch_length=0.0142054862889, name='Inner2')
             Clade(branch_length=0.239265540676, name='Inner1')
                 Clade(branch_length=0.0853101915988, name='Epsilon')
                 Clade(branch_length=0.136912030623, name='Delta')
             Clade(branch_length=0.292306275042, name='Alpha')
         Clade(branch_length=0.0747705106139, name='Beta')
         Clade(branch_length=0.175229489386, name='Gamma')

Link to this section Summary

Functions

__init__()

Initialize the class

_height_of()

Calculate clade height — the longest path to any terminal

nj()

Construct and return an Neighbor Joining tree

upgma()

Construct and return an UPGMA tree

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function _height_of()

Calculate clade height — the longest path to any terminal.

Link to this function nj()

Construct and return an Neighbor Joining tree.

:Parameters:

distance_matrix : DistanceMatrix
    The distance matrix for tree construction.
Link to this function upgma()

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.