My tree is rooting too early, and the temporality of this one does not match the existing BEAST tree.
So I thought I could add a fixed clock-rate. using
However, this goes against the relaxed clock model, so according to the treetime documentation (treetime.treetime — TreeTime 0.9.0-b.2 documentation), it is possible to take this model into account.
Do you know if it is possible to use the relaxed clock model through augur refine?
I think this issue on treetime Github should answer this question, at least with respect to treetime behaviour with fixed clock rate and relaxation on: Question about --clock-rate and --relax behavior · Issue #85 · neherlab/treetime · GitHub
TLDR; it should work if you use treetime directly, but is not tested.
Looking at the
augur refine docs, it doesn’t look like you can specify that treetime should be run with a
--relaxed clock. But maybe I’m wrong. @rneher should know. I’m also not sure what the default is for treetime run through
refine. It doesn’t look like a relaxed clock is used when running through
refine, but again, I may be wrong.
Thank you @corneliusroemer I’ll give a try.