I have been going through the "Hyphy: Hypothesis testing using phylogenies" document while making the examples on my computer. I noticed a problem with the empirical Bayes analysis.

When I created the new variable beta-alpha, I obtained 16 identical values, which was not at all coherent with the following step of the example. Upon closer inspection, I noticed that this value was equal to the first value of beta (about 0) minus the first value of alpha (about 0.24), so -0.24.

I'm afraid I might have the same problem if I do the analysis on my data.

Julie

Hi Julie,

Thanks very much for reporting this bug. I have fixed the issue and the example should work fine if you download the latest 2.0 version. HyPhy is constantly being updated and sometimes code changes introduce unanticipated bugs -- as was the case here.

Sergei