The program provides universal codon option and other options which don't seem to be applicable on my dataset. I am at a loss regarding hyphy usage on non-coding dataset as well positive selection using suitable options e.g., 'yangnielsienbranchsite2005.bf' or else? I am in dire need to get this fixed.
I don't know the HyPhy batch language well enough to make a file, but it should be possible to run this kind of analysis. The steps would be
For each site you want to create an alignment of your 'focal sequence' and the appropriate null and link each of those to a tree.
Fit whatever nucleotide model you like (F81 HKY, REV...) to each alignment given the tre, and store the maximized likelihood.
Add a constraint, such that the rate of evolution in your first alignment should be equal to rate in your second, and fit the same nucelotide model under this constraint
Use a likelihood ratio test to see whether the unconstrained model fits the data signifcantly better than the "rates equal" model
