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!