only transversions

[micheldd1978]

Hello,
My data have saturation in third position of codon, but transversions has not saturation. How can I use only transversions in MrBayes?

[nylander]

Dear @micheldd1978
A central part of probabilistic analysis is to find a model that "fits the data". Under a Bayesian setting, you have the power to do that (in a sense) by, for example, saying that "I think X is a more important part of the model" and change the prior assumptions of the analysis. I have not explicitly tried to accomplish what you are aiming for, but take a look at the output from help prset , especially for options Tratiopr and Revmatpr. They may give you some ideas.
Yours
Johan