Hi- I'm new to playing with HyPhy and have a question about the sliding window analysis output file.  Is "R" the transition/transversion rate?  I suspect it is, but in my analysis I'm getting very low values of R (well below 1), which is not what I expected.  Do you have any insight for these results?  Thanks!

If you were using the HKY85 model, then R is actually the transversion/transition ratio (for speeding up optimization), and thus can be expected to be less than one!

One can look at the actual rate matrix when in doubt with Mac and Windows versions:

• Go to Window->Object Inspector
  
• Switch to Models in the pull down of the window that pops up
  
• Scroll down until you see an entry in bold (bold means this model is being used in active analyses).
  
• Double click on the entry and take a look at the matrix to check what parameters mean what
  

There is more detail about how to inspect model parameters in the HyPhy primer:
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HTH,
Sergei