Modify the following program to takes aligned sequences from
a FASTA file and create a 2 dimensional matrix D. Each entry Dij in
the matrix is the Jukes Cantor evolutionary distance give

Dij = -3/4 ln(1 - (4/3)*pij)

where pij is the number of mistmatches divided by alignment length.

BEGIN:

import math
#Read sequence names from FASTA file
names = []
f = open("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])
    seqs.append(file2[i+1])

#Initialize variables
rows = len(file)
D = []
for i in range(0, rows, 1):
    l = file[i].split()
    for j in range(len(l)):
        l[j] = float(l[j])
    D.append(l)

END

Submit hardcopy in class on April 5th, 2016