Include fitness estimates for ORF9b, which overlaps in reading frame with N. See #21.
This generalizes the method for handling overlapping reading frames.
The GTF is now edited by a new rule after download to add ORF9b.
Numerical results for all sites change very slightly as this slightly changes the four-fold synonymous site classifications which leads to very slight shifts in the four-fold degenerate site mutation rate estimates that propagate through the analysis. However, these shifts are basically imperceptible unless you look out to several decimal points.
There is now a ORF9b heat map and it is included in the gene distribution plots.
Include fitness estimates for ORF9b, which overlaps in reading frame with N. See #21.
This generalizes the method for handling overlapping reading frames.
The GTF is now edited by a new rule after download to add ORF9b.
Numerical results for all sites change very slightly as this slightly changes the four-fold synonymous site classifications which leads to very slight shifts in the four-fold degenerate site mutation rate estimates that propagate through the analysis. However, these shifts are basically imperceptible unless you look out to several decimal points.
There is now a ORF9b heat map and it is included in the gene distribution plots.