I'm a PhD student and read your tutorial about MrBayes softwar. for my thesis, I working with MrBayes software to analyzing data. your help and guidance are valuable for me.
I have a question about substitution model for mrbayes software. I use jModeltest to determine the best model for my sequences. and the TPM1uf + I + G is the model I got form jModeltes (BIC).
MY question is: How can I apply the model which determine by jModeltest in MrBayes software.
for example : the model TPM1uf + I + G and parameters: nucleotide frequencies A: 0.27, C: 0.19, G: 0.17, T: 0.37; substitution rates RAC: 1, RAG: 13.33, RAT: 4.63, RCG: 4.63, RCT: 13.33, RGT: 1; gamma distribution shape = 0.48; and proportion of invariable sites = 0.38 .
Is it mean that I apply the substitution rates through Ravmatpr=fixed (1,13.33,4.63,4.63,13.3,1) or Ravmatpr is different parameter from substitution rate?
and is it necessary to apply nucleotide frequencies by statefreqpr=fixed(0.27, 0.19, 0.17,37) also for gamma distribution shape and proportion site ? also, If I used nst=mixed to estimate substitution model by Mrbayes, it is still necessary using Jmodel test or mrmodeltest?
thanks in advanced