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.