#NEXUS

[ Example command file, which reads in a data file and sets up different codon models.
  Use one of the blocks to set up the model you are interested in. ]

begin mrbayes;
	[The following line is useful for automatic execution with no
	 warnings issued before files are overwritten and automatic
	 termination of chains after the prespecified number of generations.]
	set autoclose=yes nowarn=yes;
	   
    [Read in a data file with protein-coding sequences]
    execute replicase.nex;

    [Use ONE of the blocks below depending one what model you like]

    [One omega value for the gene
     The estimated single omega value, valid for
     the entire gene or gene fragment, is printed
     to the .p file(s)]
    lset nucmodel=codon;

    [Omega variation across sites with three classes,
     omega_1 < 1, omega_2 = 1, omega_3 > 1.
     The estimated omega_1 and omega_3 are printed to
     the .p file(s) as omega(-) and omega(+).
     If you set report possel=yes, you
     will also get the probability of each site being in
     the positively selected omega class.
     If you set report siteomega=yes, you
     will also get the omega value for each site.]
    lset nucmodel=codon omegavar=ny98;
    report possel=yes;
    report siteomega=yes;
    
    [Omega variation across sites with three classes,
     omega_1 < omega_2 < omega_3. Otherwise very similar
     to the Nielsen and Yang model.]
    lset nucmodel=codon omegavar=m3;
    report possel=yes;
    
    [These models are slow, so print to screen more frequently]
    mcmcp printfreq = 10;

    [Only the mcmc command is missing now to run the analysis]
end;