Entering edit mode
12.1 years ago
Rahul Sharma
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660
HI, I am using codeml in my analysis. I have some basic question regarding the "fix_omega and omega" parameters of codeml file. It would be great if someone could explain the use of these parameters.
Hi Rahul, this question is very general. Fix omega does what is says, fixes one of omegas in the model to a particular value (set by Omega). What in particular are you struggling with?
Hi David, Thanks for your reply, actually I want to predict the positively selected genes in four closely related genomes. I was using Branch-site model 'Test-2' for this purpose. In this test I was using "fixomega and omega" parameters. Can we conclude that the sites with labeled branches are under positive selection, if our LRT H0(wfix=1) and H1(w_fix=0) test comes significant i.e p-value < .001. Or should I also try free-ratio and one-ratio tests ??? Thanks in advance