I would use the ModelTest to observe what would be the model of nucleotide substitution for my datasets, and I noticed he left a version with GUI and now more user-friendly, well I ran the test and the result came out with the AIC. But the model suggests that it does not match those of the HYPHY, I say this because, for example when choosing rate parameters, the user option, the HYPHY already placed on the AG, fixing him in 1.0000, when for example the result of Jmodeltest the value 1.0000 is AT = GT, as follows:

Model selected:
   Model = TPM3uf+G
   partition = 012012
   -lnL = 10499.5544
   K = 154
   freqA = 0.3723
   freqC = 0.1491
   freqG = 0.1598
   freqT = 0.3188
   R(a) [AC] =  1.6489
   R(b) [AG] =  13.1093
   R(c) [AT] =  1.0000
   R(d) [CG] =  1.6489
   R(e) [CT] =  13.1093
   R(f) [GT] =  1.0000
   gamma shape = 0.3080



My question is: How can I use the JModeltest results to set up HYPHY?

Best Regards,

Jackson Lima