When I have a moment I will fill in the blanks
You must have an RNA virus (nothing else will mutate that fast). The basal group and root is the USA. It estimates the time to that basal event is 32.3 (likely years).
"frequencies" frequency of ACGT where the missing one will be 0.25.
Its a simple model of constant population size.
ESS is the most important parameter to ensure convergence of the Bayesian simulation .
Likelihood is the second most important parameter. I'll edit again shortly.
I'll fill in one more blank and summarise ...
This will be the transition transversion ratio in HKY. I suspect it also will be transition transversion ratio in Kimuras 3-parameter model, this is because ... the transversions are further split into two mutation groups, ie. purine to pyrimidine has 2 further combinations and you end up with 2 ratios. that makes sense, transition/transversion (kappa 1), transition/transversion 1 (kappa 2), transition/transversion2 (kappa 3) ....
- CP1.kappa 18.716
- CP2.kappa 17.16
- CP3.kappa 22.796
CP2 and CP3 are either side of CP1 .. which is what you would expect on my interpretation.
These are very high values by the way, essentially there are very few transversions in this data, so ... I dunno. You need to check the data, if you see lots (and lots) of A-G and T-C mutations, then thats what I believe it is saying.
Briefly posterior and prior are the fundamental method of a Bayesian calculations, the output is probability expressed as a log, so the more negative the higher the probability (the prior looks like a random tree, or a reasonable tree with really rubbish parameters, likely the former).
Essentially I am going to call it a day here. The real issue is that the output summarise the entire modern theory in phylogenetics, so its a very long response required to address all of the parameters and I honestly don't think it helps your analysis. What I am clear about is:
* You've omitted a gamma distribution (I think Tracer would summarise this) *
So my advice is:
- ESS MUST be homogeneous between runs - big trouble if not
- gamma distribution MUST be run
Beast can be tricky getting gamma to converge via ESS, just a word of warning.
I can't see the full robustness, because its absent... However, from the output, I think its pretty clear, that you (well me) can more or less see the model you ran.