Write a Python program that takes as input a FASTA file of unaligned
sequences and outputs the neighbor joining tree. Modify the function
for computing Jukes Cantor distances to first align and then compute the
distance. Modify the UPGMA_from_sequences.py program to complete this 
assignment. First make sure that your neighbor joining program is 
working by testing it on the Haemoglobin example shown on the website.

Submit one .py file containing all your solution. This means the
functions that you use must also be in this file. 

Test your program on the example shown on the website. 

We will test your program on a different dataset unknown to you. 

HOW TO SUBMIT YOUR ASSIGNMENT:

Copy your solution to your course directory 

/afs/cad/courses/ccs/s14/bnfo/136/002/<UCID>

Use the Unix command 

cp <yoursolution>.py /afs/cad/courses/ccs/s14/bnfo/136/002/<UCID>/

DUE DATE: 2:30pm, May 10th, 2014

Good luck!