Sorry for this additional question--I'm very grateful for this discussion group, the manual, and the recent Álvarez-Carretero et al. paper!
I recently performed the branch test on a set of genes. I noticed that some branches I marked as foreground were significant (i.e., significant p-value from log likelihood test) but I noticed the omega value was not greater than 1, indicating positive selection. I was wondering how I should interpret my results--for example if for alt M2 the results were w0=0.0153 and w1=0.6435 while the null M0 w0 for all branches=0.0234, could you infer that the foreground is under relaxed purifying selection (but not strong selection, since it's less than 1?) Because it was a significant log likelihood result, it appears there is evidence that the alt model better explains the data than the null model/reject a single rate of evolution for all branches.