Dear JH,

If you have two trees:

Tree t1 = (in1,in2,out);
Tree t2 = (in1,in2,out);

under the HKY85 model with a branch length parameter t and global tv/ts ratio of R (assume that R is the same in both data sets), then imposing a relative ratio constraint is going to be equivalent to setting

t1.in1.t := C * t2.in1.t;
t1.in2.t := C * t2.in2.t;
t1.out.t := C * t2.out.t;

where C is the proportionality parameter estimated from the data (thus the 2DF test).

You are correct that the Relative ratio test will constrain all branches (and not just the outgroup).

Unless you have a 4th sequence (or use a non-reversible model), all you can test regarding the outgroup is the amount of divergence from the MRCA of (in1,in2) - since you can't root the 'out' branch.

It sounds like what you are trying to do is test whether the ratio

t1.out.t/t1.in1.t = t2.out.t/t1.in1.t

(this assumes molecular clock on in1, in2) or something like for the general case

t1.out.t*2/(t1.in1.t+t1.in2.t) = t2.out.t*2/(t2.in1.t+t2.in2.t)

I am linking a human/chimp/mouse example with both of the above constraints defined (using the GUI).

Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Let me know if this helps/addresses your question.

Cheers,
Sergei