I am running codeml on orthogroup tree to determine whether a certain lineage is under positive selection. The way I did is to set null model with fixed omega (model=2, NSsites=0, fix_omega=1) while branch-specific model by labeling branch of interest (foreground) in tree file (model=2, NSsites=0, fix_omega=0). After running codeml on both models, I was able to extract likelihood (lnL) and number of parameters (np) for each model, as well as Kn/Ks value for background branches and foreground branches in branch-specific model.
To found out the significant difference on Kn/Ks values between foreground and background branches, I calculate LRT by LRT=2*(lnL1-lnL0) and corresponding pvalues using dchisq function (df =1) in R. I noticed that in some orthogroups, LRT was reported as a negative value which leads to pvalue =0. That is definitely abnormal. How could LRT being negative happen?
Also, I am still a little bit confused about Kn/Ks value predicted for background and foreground in branch-specific model report. If I compared them and Kn/Ks is larger in foreground compared to background, may I make a comment that lineage I chose is under positive selections? The other way around, if Kn/Ks is smaller, the lineage is under negative selection.
Hope I have made my question clear. Thank you