Some problems about CODEML
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5.8 years ago
Ginsea Chen ▴ 130

Dear All !

I tried to use codeml to detect positive selection sites along my interested branches (thereafter these branches). First, I performed "two-ratio" model (branch model) analysis with setting these branches as foreground branch. The LRT statistics showed that "two-ratio" model differ significantly with "one-ratio" model, and omega value of foreground was higher than 1 (about 2.5). So I concluded that these branches evolved under positive selection pressures. While I have no positive selection sites identified by using branch site model analysis with setting these branches as foreground branch, and correspondent LRT statistics result was non-significant (Model A vs Model A null). I don't know how to explain this result. If you have some suggestions, please tell me.

Thanks all.

CODEML Positive selection sites PAML • 1.8k views
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