Complete the program below to compute the evolutionary distance
between two sequences using the formula:

            (           Unique common kmers between x and y        )
d(x,y) = -ln(                   --------------------               )
            (  			Min(len(x), len(y))		   )


Submit hardcopies in class on Apr 14th.

BEGIN

names = []
seqs = []
f = open("sequences.fasta")
file2 = f.readlines()
f.close()
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])

number_of_leaves = len(seqs)
number_of_nodes = 2*number_of_leaves - 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]
#        [aligned_seq1,aligned_seq2] = alignment.NWalignment(seq1, seq2)
#        for k in range(0, len(aligned_seq1)):
#            if (aligned_seq1[k] != aligned_seq2[k]):
#                mismatches+=1            
#        Dij = (-3/4)*math.log(1-(4/3)*(mismatches/len(aligned_seq1)))
        blast_score = alignment.blast_like_alignment_fast(seq1, seq2)
        Dij = -1*math.log( common kmers betweem seq1 and seq2 /
                            min(len(seq1), len(seq2)))
        l.append(Dij)
    D.append(l)
                                  
#for i in range(0, len(D)):
#    print(D[i])

END