Examining Score Matrices

Now do the same as you did before but without the -p option:

% ./JTT

1. Question 6: What are the two main differences you notice between the substitution matrix and the score matrix? Write your answers.
   
   
2. Have a look at JTT 40. Question 7: a) Are any entries positive off the diagonal? b) What does this mean in terms of exchange of amino acids in homologs versus random chance? Write your answers.
   
   
3. Find the log-odds of V going to I or vice versa in JTT40. Q8: Why does it make sense that this is positive? Write your answers.
   
   
4. Take the least and most mutable amino acids from your answer to Q4. Q9: how do they compare in terms of number of positive entries? You can use columns or rows to compare, it doesn't matter. Again, please write your answers.
   
   

Next we'll use a program to compute evolutionary distance for some of our real data and our evolutionary data.