Hi Flu,

The version of BS-REL implemented in version 2.2 of HyPhy is quite different from 2.1.2 and the Datamonkey version. Whereas the old version used 3 dN/dS classes per branch, the new model adaptively chooses the number of rate classes, resulting in a simpler model. How different were your results? Did the 2.2 version detect more branches under selection?

Sergei

Hi Sergei,

I have now obtained the results from rerunning the data set in HYphy (BS-REL  program) when "allowing Branch-site variation in synonymous rates" and the outcome was that NONE of the branches were affected by episodic diversifying selection.

For the same dataset the following results are obtained with regard to the number of branches affected by episodic diversifying selection:

1. Datamonkey (BS-Rel program)  15 branches.

2. Hyphy (BS-Rel program; NOT allowing Branch-site variation in synonymous rates)      18 branches

3. Hyphy (BS-Rel program;  ALLOWING Branch-site variation in synonymous rates)        0 branches

Which of these 3 approaches is preferred? Does situation 3 mean lack of power and situations 1 and 2 many false positives or...? I am not sure how to interpret the above results. I expect situation 3 to differ from situations 1 and 2 but not as drastically as the outcome is in this particular analysis.  I very much appreciate your input and I can send you the data set if you want to look at it further?

Thank you very much in advance for your input.

Best,

Flu

Thanks Sergei for your suggestion.

Best,

Flu