Question: Fixing Omega Values In Codeml
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gravatar for RT
6.4 years ago by
RT340
European Union
RT340 wrote:

Dear All,

I have seen in few examples/tutorials that while doing the codeml analysis each model is run using more than one Omega value (0,1,2,10 or so in control file). What does that mean? I get exactly same results when I vary the omega values.

Someone specified on a blog that 'more branches shows positive selection as the initial omega is greater'. HOW?

Just read from the Paml documentation that the variable fix_omega fixes the last omega ratio (omegak-1 if you have k ratios in total) at the value of omega specified in the file. I don't understand this. Can anyone please help!

Thanks

codeml • 2.2k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 6.4 years ago by RT340
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