I'd like to ask for advice about how to check if the synonymous rates in my alignment/tree set are saturated or not, and hence whether it makes sense to calculate the dN/dS at all.
I would like to get a single dS rate for my data, averaged across branches and sites. I played around with Hyphy (learning the script lingo helps a ton in the long run), and got the one-ratio model to work, but this only gave me the ratio, not its individual components. The more sophisticated analyses (branch- or site-specific) do return those values, but I am not sure if it would be valid to simply average them out, especially if they might come from different distributions.
Any help would be appreciated.

EDIT1:
Hokay, I looked around the forums a bit more and found 2 topics on the subject:

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The second one suggested using the dSdN.bf script to get individual dN and dS values, which I downloaded and run. Now my question is, if would it be proper to just average out all the branch-specific dS and dN estimates and get a single value +/0 SE?
The script was not present in the latest git version of Hyphy, so I would assume there is reason for it to be excluded?

EDIT2: After looking into the source of dSdN.bf, it occured to me that it is supposed to open some windows, but when I run it from the cmd-line, it does not do that. What might the problem?