begin mrbayes;

	set autoclose=yes nowarn=yes;

	
	log start filename=NAME.txt replace;

   [

[defines partition according to codon position]	
	charset first_pos  = 1-1131\3;
	charset second_pos = 2-1131\3;
	charset third_pos  = 3-1131\3;
	partition by_codon = 3:first_pos,second_pos,third_pos;

[sets partition according to codon position]
	set partition=by_codon;

[APPLIES Kimura? model to 1 and 2nd positions and gtr+|~+I model to 3rd codon position]	
	lset applyto=(1,2) nst=2;
	Lset  applyto=(3) nst=6  rates=invgamma;[ from MrModeltest, hLRT = AIC]

[to unlink codon position such that each has its own set of parameters]		
	unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);	

[fix the statefreqs to equal for the first two codon positions but applies a flat Dirichlet prior to the state- freqs of the 3rd position]
	prset applyto=(1,2) statefreq=fixed(equal);
	prset applyto=(3) statefreq=dirichlet(1,1,1,1);


   ]

	outgroup 1;	

	mcmc ngen=10000 printfreq=100 samplefreq=100 nchains=4 temp=0.2 swapfreq=1 savebrlens=yes;

	log stop;


	sump burnin=1000;

	sumt filename=name.nex contype=allcompat [conformat=simple] burnin=1000 nruns=2;


end;