Which substitution rate is which, in the model output?

[Teresa Pegan]

Hello! I was able to run modestest-ng and I got this as some output:

Model:              TIM1+I
lnL:                -16737.2351
Frequencies:        0.2856 0.3252 0.1401 0.2491
Subst. Rates:       1.0000 23.1701 0.3250 0.3250 12.1937 1.0000
Inv. sites prop:    0.8724

I can see that the output includes 4 frequencies and 6 substitution rates, which I assume correspond to the 4 base pairs and the 6 possible base pair substitutions, respectively. My question is, which frequency and which rate is which? I.e., what is the order of the 4 bases and the 6 base combinations that correspond to those numbers?

With TIM+1, I know from the documentation https://github.com/ddarriba/modeltest/wiki/Models-of-Evolution that this model estimates substitution rates like this: AC=GT ; AT=CG ; AG ; CT. So, the rates with values 1.000 and 0.3250 must belong to those ones that are set as equal to each other. But I don't know which is which, or which rate belongs to CT and which to AG. It seems that the rates are not given here in the same order as they were in the documentation, otherwise rates one and two would be the same (AC=GT), as would rates two and three (AT=CG). 

Apologies if I missed this information somewhere in the documentation. I looked for it and could not find it.

Also, please disregard my previous message to this group about JmodelTest, I have now realized that modestest-ng replaces it. I would recommend writing a message on the JModelTest GitHub page pointing people to modestest-ng. Lots of tutorials still point people to JModelTest, and it took me a while to realize that it's not really supported anymore.

Thanks!

-Teresa