TreeConstructionDistanceBased.py

# Import modules
from Bio import Phylo
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
from Bio import AlignIO

# Read the sequences and align
aln = AlignIO.read('msa.phy', 'phylip')

# Print the alignment
print aln

# Calculate the distance matrix
calculator = DistanceCalculator('identity')
dm = calculator.get_distance(aln)

# Print the distance Matrix
print('\nDistance Matrix\n===================')
print(dm)

# Construct the phylogenetic tree using UPGMA algorithm
constructor = DistanceTreeConstructor()
tree = constructor.upgma(dm)

# Draw the phylogenetic tree
Phylo.draw(tree)

# Print the phylogenetic tree in the terminal
print('\nPhylogenetic Tree\n===================')
Phylo.draw_ascii(tree)