Codeml Fix_Omega And Omega

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11.5 years ago

Rahul Sharma ▴ 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.

codeml selection • 2.6k views

ADD COMMENT • link 11.5 years ago by Rahul Sharma ▴ 660

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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?

ADD REPLY • link 11.5 years ago by David W 4.9k

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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

ADD REPLY • link 11.5 years ago by Rahul Sharma ▴ 660

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