I have been running PAML, via codeml, to try to identify positive selection in certain branches of my tree for one gene (but will eventually be trying to automate the analysis over multiple genes). This was done by setting
model = 2 and
NSsites = 2 in the codeml.ctl file. I attempted to run both the null and alternative models by setting
fix_omega = 1 in the null.ctl and
fix_omega = 0 in the alternative.ctl.
However, after running both models, they have returned exactly identical log-likelihood (lnL) values. I wasn't expecting to find anything significant, but the fact that they were identical struck me as odd. Out of curiosity, I altered the branch of interest in the newick tree file and reattempted the analysis, but again, the lnL values remain the same between the null and alternative models (although slightly different to the value returned with the different branch selected).
I have since repeated this many times, choosing a different branch(es) each time to see if I can get a difference between the null and alternative, but no luck. Am I missing something obvious? Should I really be getting the same exact result between null and alternative models, regardless of where in the tree I place
#1? To reiterate, I wasn't expecting to find significant results, but was at least expecting (non-significantly) different numbers for lnL...