Testing Evolutionary Hypothesis ( branch-sites )

Question

[Juke34]

Hy community! I am testing Evolutionary Hypothesis, I have tried two model bsA (positive-selection / branch-site) and bsA1 (relaxation / branch-site) and I get exactly the same log-likelihood value. What could it means? It is something that happens often when comparing different models?

As the two log-likelihood values are the same I guess the chi test cannot be perform, so should I consider the p-value as 1meaning my null hypothesis (bsA) cannot be rejected?

[manaswwm]

I personally never used these models on codeml, but from your wordings I think it means that the analysis is not able to distinguish whether the signal coming from your sequences is that of a relaxed constraint or positive selection. This is so because relaxed constraint and positive selection, both, leave similar signatures (increased substitutions). The only inference that I can draw from this is that there is not a sufficient amount of proof to infer that positive selection is predominant and that relaxed constraint cannot be ruled out. I think the said models originate from this paper, which might be of more help in your case, especially the discussion sections (I think what they refer to as "test1" and "test2" is "bsA" and "bsA1")