Write a Python program to that takes as input a set of aligned
DNA sequences and outputs the maximum parsimony tree as given
by an NNI-based local search. Use the pseudocode below that we 
also discussed in class.

BEGIN CODE

Read aligned sequences from file in FASTA format
Make a random tree T
done = 0

while(!done){
  for(i = nleaves to total_nodes){

     score1 = smallparsimony.parsimonyscore(T)

     NNI(T, i, 0)

     score2 = smallparsimony.parsimonyscore(T)

     if(score2 < score1) { i = -1; break; } #exit loop
     else { undo NNI move by calling NNI(T, i, 0) }

     NNI(T, i, 1)
  
     score2 = smallparsimony.parsimonyscore(T)

     if(score2 < score1) { i = -1; break; } #exit loop
     else { undo NNI move by calling NNI(T, i, 1) }

     if(i == total_nodes) { done = 1 } #this means we have done one pass
				   #of the tree without finding a better
				   #score and so we are done with the search
  }
}

Your completed program is due March 6th 2018. 

Submit your program in the directory /afs/cad/courses/bnfo/s18/bnfo/602/002

END CODE