Dear Scott,
Firstly, did you, declare r and r1 as global variables?
global r;
global r1;
The code may behave incorrectly if you didn't.
Secondly, the test as set up, will test whether branches A,B,C are evolving at a relative rate different from the rest of the branches, assuming that the relative ratio test hypothesis (using your synonymous tree as a reference) is valid. I think this is what you want to test, so all seems well.
Thirdly, the 'r' (and 'r1') parameter will also include a multiplicative 'branch scaling factor' (since Branch Length = c * t, where c is some constant determined by substitution biases and base composition, and will depend on the model), hence it is not directly comparable to 1. To rescale it after optimization, you can use something like
Code:rescaled_r = r*Tree_13.A.t/BranchLength (Tree_13,0)/
which will multiplies r by the reciprocal of 'c' in the BL = c*t relation.
Cheers,
Sergei