I am working with nextstrain in my lab to visualise our viral strains.
I really am trying to make the frequency panel work and thanks to this forum i got that working.
However my panel is only showing me the tip frequencies.
When i looked in the documentation, i added --include-internal-nodes but this did nothing to the panel. also --inertia= 1 does nothing?
am i missing something? are the internal nodes not calculated ?
As you can see in 1997 there is i mutation into the AA : I but it is not shown on the frequency panel. I have been breaking my head over and over to see if something would change the outcome.