Hello everybody,
I am conducting a study to identify selected positive sites in a group of proteins using the Branch-site model implemented in Codeml-PAML. When I compare the null model to the alternative model using chi-square, it returns a significant p-value of 0.01. It means that the selected branch presents evidence of positive selection. However, when I search for the amino acid under positive selection in the BEB analysis, it shows a list with all amino acids studied and none of them have significant values, in fact, all values are below 90% probability. In contrast, the NEB analysis shows several amino acids under positive selection with probabilities greater than 95% and 99%. How can I interpret these results?
Best regards
Daniel
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