Issue with Interpreting Codeml Output from PoSeiDON

[Dx-wmc]

I am using PoSeiDON for positive selection analysis, as mentioned in a recent publication (https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012161). The software successfully generated multiple codeml output files (.mlc files), but I am having trouble interpreting them and applying the empirical Bayes approach mentioned in the paper: "we used an empirical Bayes approach to calculate posterior probabilities that a codon coming from a site class with dN/dS>1. Genes were considered to be positively selected when the p-value is <0.05 and the dN/dS ratio exceeds one."

Could you provide guidance or examples on how to proceed with analyzing these .mlc files to identify positively selected genes based on this approach?