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@Vini2
Created March 23, 2018 20:00
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# 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)
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