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#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;
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