The varying mutation rates for mpox is getting me very confused about augur refine step.
If I have a mpox tree with a mix of samples from inside and outside of the current outbreak, for augur refine is it appropriate to use (copied from Nextstrain’s mpvx tree build here)
clock_rate: 3e-6
clock_std_dev: 6e-6
or should I leave these blank so it’s calculated using samples on the tree?
Also does anyone have a sense what clock_filter_iqd would work well to remove outliers in this case? Or is there a way to plot the distribution so I can see a normal iqd…
Thanks very much!