Q:

Infer distance since duplication from tree? 

Question
I have a really simple question, but I'm not able to figure it out.  
I made a tree (using BLOSUM62).  Here is a part of the tree:

How can I calculate the distance till the duplication event occured between HBD en HBB? 

just for HBB 36.21 and for HBD 38.79
or 38.79 + 36.21 = 75

More info
I determined if this set of sequences follows a molecular clock, and indeed this was the case.  So I determined the rate at which these sequences envolve.  If I can determine the distance between HBD and HBB I can devide this by the rate to obtain the time since the duplication event happened. 

How could you calculate this one? 

A:

Assuming a molecular clock, the distance between the sequences and the duplication event is 75/2 = 37.5.  Ideally, these sequences should have the same distance from the internal node (under a clock), and you could use a model that explicitly assumes a clock -- which will lead to ultrametric trees.   One example is the program promlk (or dnamlk) from the phylip package.  A faster alternative would be the  UPGMA method, which also gives you an ultrametric tree.