phylogenetic tree code.txt

import Bio as Bio
from Bio import SeqIO # for reading and writing sequence files in various formats
from Bio import AlignIO 
from Bio import Phylo # for working with phylogenetic trees

s1 = SeqIO.read("sequence1.fasta", "fasta")
s2 = SeqIO.read("sequence2.fasta", "fasta")
s3 = SeqIO.read("sequence3.fasta", "fasta")
s4 = SeqIO.read("sequence4.fasta", "fasta")
s5 = SeqIO.read("sequence5.fasta", "fasta")
s6 = SeqIO.read("sequence6.fasta", "fasta")

print(s6.description)

s1.id = 'Angel_Shark'
s2.id = 'Gray_Reef_Shark'
s3.id = 'Mako_Shark'
s4.id = 'Tiger_Shark'
s5.id = 'Great_White_Shark'
s6.id = 'Hammerhead_Shark'


sharks = SeqIO.write([s1,s2,s3,s4,s5,s6], "sharks.fasta", "fasta") # Write them into one file


# Path: sharks.aln 
# https://www.ebi.ac.uk/Tools/msa/muscle/
# use it for alignment of the sequences in sharks.aln

with open("sharks.aln","r") as aln: 
    alignment = AlignIO.read(aln,"clustal")
print(type(alignment))



from Bio.Phylo.TreeConstruction import DistanceCalculator 
calculator = DistanceCalculator('identity')


# distance matrix is a square matrix of distances between all pairs of sequences in the alignment 
distance_matrix = calculator.get_distance(alignment)
print(distance_matrix) # print the matrix


from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
constructor = DistanceTreeConstructor(calculator)


shark_tree = constructor.build_tree(alignment)
shark_tree.rooted = True
print(shark_tree)


Phylo.write(shark_tree, "shark_tree.xml", "phyloxml")



import matplotlib
import matplotlib.pyplot as plt


fig = plt.figure(figsize=(13, 5), dpi=100) # create figure & set the size 
matplotlib.rc('font', size=12)              # fontsize of the leaf and node labels 
matplotlib.rc('xtick', labelsize=10)       # fontsize of the tick labels
matplotlib.rc('ytick', labelsize=10)       # fontsize of the tick labels
#turtle_tree.ladderize()
axes = fig.add_subplot(1, 1, 1)
Phylo.draw(shark_tree, axes=axes)
#plt.savefig(output_file)



Phylo.draw_ascii(shark_tree, file=None, column_width=80)


# for saving the figure
fig.savefig("shark_cladogram", dpi=100, bbox_inches='tight')