Write a Python program that takes a set of whole 
genome sequences in FASTA format and outputs a UPGMA tree
in newick format with species names included.

In your program first determine the distance matrix with the
formula

            (           Number of unique common kmers between x and y        )
d(x,y) = -ln(                 --------------------------------               )
            (          Min(number of uniq kmers(x), num of uniq kmers(y))    )

You will have to find the unique common kmers of length 9 between 
x and y. Use the fast_blast_alignment.py program on the course website
to determine unique common kmers of length 20.

Then run UPGMA on the distance matrix.

Make sure the output is in newick format with species names.

Your completed program is due May 2nd 2018.

Copy your upgma_genome.py program into 
/afs/cad/courses/bnfo/s18/bnfo/602/002/<UCID>/ where we will run 
it for evaluation.