Dear Sergei,

Before I start, I would like to let you know that I am an absolute beginner. So please don't be annoyed if my questions seem too trivial to you.
I have an alignment of bacterial sequences and I believe there could be some dual coding region in somewhere close to middle of the alignment. I started to look if there are some models in HYPHY which would allow me to check this.  And I found this post where you have a pretty long conservation
( conversation number- num=1149266253/4#4, sorry but I was not allowed to post the URL in this message)

However, as you suggested, do we really need to complicate things with such models ?
I think a relatively simple thing to do is to just look at the rates of synonymous substitutions in one of the frames. If there is indeed dual coding, I should see a much reduced rate of synonymous substitutions in this region. Because synonymous positions in one of the frames would be non-synonymous in the other reading frame.

So I believe I should use dNdSBivariateRateAnalysis.bf to see if there is variation in Ks.
Do you have something to suggest ? I have some technical questions as well but I would like to be sure first that I am doing things the right way.

Thanks and regards

Sankalp