Dear Chris,

Firstly, I assume that you have the sequence data as well, so you can run additional ML model fitting. Secondly, I surmise that you are interested in testing whether mean branch lengths differ between clades, or something along those lines?

In the context of formal hypothesis testing, you could try setting a constraint that the means of branch lengths over clades are the same, versus the general case of free model fitting and then using the LRT to test for significance. One can also similarly test whether mean pairwise distances between all leaves in a subtree are the same among two clades.

If this makes sense and answers part of your question, I can provide details of how this type of constraint can be set up in HyPhy.

Cheers,
Sergei

P.S. The analysis to compare MEAN branch lengths between two or more clades (non-nested) in a tree using an arbitrary nucleotide model can be downloaded from Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login. The tree input for this file should have roots of the clades marked by CladeN (where N is a number), as in:

((a,b)Clade1, (c,d), (e,(f,g)) Clade2, h)