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?

Dear Hiacynt,

Calculating dS separately is not the best way to check for saturation. Instead, I would run the analysis that you want to run, then check whether the synonymous rate inferred under that analysis goes to infinity (the hard limit in HyPhy being 10000). This tells you whether the data are saturated _for your purpose_.

Averaging branch-specific estimates is in general _not_ correct (e.g. the branches might have different lengths so you clearly shouldn't be averaging using equal weights).

dSdN.bf was never included in the HyPhy distribution - it was always separately downloadable.

The command line version of HyPhy does not support the opening of windows; scripts doing that require the GUI version.

Hope this helps,
Konrad Scheffler