[BMI776] Note on HW2

[Colin Dewey]

Hi all,

Just one note about HW2 Problem #1:

It is critical that you simulate the character states at the internal  
nodes as well as at the leaves.  You will not report the states at the  
internal nodes in the output, but they must be simulated in order to  
get the correct distribution over leaf nucleotides.

For example, suppose that at one position in the root sequence you  
have an 'A'.  You would first simulate the state at the node that is a  
parent of X_1 and X_2, using branch length 0.3.  Suppose you sample a  
'C' for this node.  Then you would sample the states of X_1 and X_2  
based on their parent being a 'C'.

Colin