Sergei Pond

Dear @kavithamallayaa, spond at temple dot edu Best, Sergei

Dear @gwct, By locus here, do you mean "gene" (or alignment)? Do you simply want to "unpack" dN/dS, i.e. get the global dN and global dS estimates? Best, Sergei

Dear @gwct, Those would be best approximated by summing `dS` and `dN` estimated for each branch in the tree in `FitMG94.bf` output `json`. You can do with the a simple...

Dear @gwct, There's no average to compute here. The quantity is aggregate over the entire tree, defined as ``` dS = expected number of synonymous substitutions / expected synonymous sites...

Dear @gwct, Correct; but the two dN/dS values will **not** be the same. The directly estimated one (form the `json`) is the one to use. Best, Sergei

Dear @dgkontopoulos, I'll look into it; can you share the input file and parameter settings? In the meantime, you can use `ENV="TOLERATE_NUMERICAL_ERRORS=1;"` command line argument with the latest version to...

Dear @jinglkang, This does seem too long. Could you share one of the files and the command you are using here, so I can benchmark it locally. Will help me...

Dear @jinglkang, Using the current release of HyPhy on an MacBook Pro with an M1 Max processor, the analysis finishes in ~4 minutes. You could be using an outdated version...

Dear @jinglkang, There is a big difference between 2.5.42 and 2.5.48 (you would notice that). I would recommend updating to the latest version, and using the commands that I provided...

Dear @Emilyaoc, Other than multiple comparisons and loss of power due to a reduced sample size (# of branches), there are no fundamental statistical issues that I see. But the...