Closed jbloom closed 1 year ago
@rneher, would you be able to point me to the file with your estimates that you were using to make the correlations between the UShER
fitness and estimates and your estimates?
Now that I understand that UShER
is masking some sites, I am fixing those in my estimates and want to see to what extent that eliminates the outliers that you flagged. I figured it would be easiest if I could just do this rather than keep having to ask you, but wasn't sure what file to use for your estimates.
Fixed in #6; sites like L5F were actually masked in the UShER
tree.
@rneher compared the method here with his method. In general in comparison to deep mutational scanning data, the method here seems to work better probably because it has better synonymous rate estimates and a much larger sequence data set. But he noticed that there were some discrepancies at a few sites as noted below. Investigate these to make sure they don't indicate some larger problem: