Modify the program below to compute the Needleman-Wunsch
alignment between every pair of sequences in the input.
Then use the aligned pair to compute the Jukes Cantor 
evolutionary distance.

Submit hardcopy in class on April 7th, 2016

import math
#Read sequence names from FASTA file
names = []
f = open("haemoglobin.aligned.fasta")
file2 = f.readlines()
f.close()
seqs = []
for i in range(0,len(file2),2):
    file2[i] = file2[i].rstrip('\n')
    names.append(file2[i])
    file2[i+1] = file2[i+1].rstrip('\n')
    seqs.append(file2[i+1])

#Initialize variables

D = []
mismatches=0

for i in range(0, len(seqs), 1):
    seq1 = seqs[i]
    l=[]
    for j in range(0, len(seqs)):
        mismatches = 0
        seq2=seqs[j]
        for n in range(0, len(seq1)):
            if (seq1[n]!=seq2[n]):
                mismatches+=1            
        Dij = (-3/4)*math.log(1-(4/3)*(mismatches/len(seq1)))
        l.append(Dij)
    D.append(l)
                                  
for i in range(0, len(D)):
    print(D[i])