Testing monophyly from per site log-likelihoods without optimising branch lengths
If you have the budget for it, I highly recommend Geneious for topology work.  It was a real saver for me on an epi paper last year.

Anyway, they allow for testing per-log likelihood without adjusting edge length.  If you want to throw up some dummy data somewhere I can throw up an example. 
I have no connection or stake with the company, just happy with it.