# Modules to build the tree
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
from Bio.Phylo import draw
from Bio import Phylo, AlignIO
import subprocess
import matplotlib
import matplotlib.pyplot as plt

alignment = AlignIO.read('tree_example.fasta', 'fasta') # reading the alignment file

calculator = DistanceCalculator('ident')
dm = calculator.get_distance(alignment) # distance matrix

constructor = DistanceTreeConstructor()
tree = constructor.nj(dm) # build with neighbour joining algorithm a tree from dm

Phylo.write(tree, 'TreeToCutOff.nwk', 'newick')

plt.rc('font', size=1)          # controls default text sizes

#HERE IS THE SETTING FOR THAT ALLOWS ME TO HIDE THE BRANCH TIP LABELS
plt.rc('axes', titlesize=14)     # fontsize of the axes title
plt.rc('xtick', labelsize=10)    # fontsize of the tick labels
plt.rc('ytick', labelsize=10)    # fontsize of the tick labels
plt.rc('figure', titlesize=18)   # fontsize of the figure title

draw(tree, do_show=False)
plt.savefig("Bioinfo_tree.png", format='png', dpi=500)

# Modified from https://bioinformatics.stackexchange.com/questions/4337/biopython-phylogenetic-tree-replace-branch-tip-labels-by-sequence-logos