I have just checked your attached input files and I can see that you are trying to use a codon model with a protein alignment. I suggest you convert your sequences and obtain a codon alignment, then try to run CODEML again under the homogenous (M0) model. There are various ways to do this but, if you want to go through the same procedure we used to analyse the example data from our "Beginner's guide on the use of PAML to detect positive selection" (
Álvarez-Carretero et al. 2023), you can then follow our step-by-step tutorial
available in our `positive-selection` GitHub repository, specifically directory `00_data`. First, you can try to follow the tutorial with our example data while following the protocol paper to get more familiar with the main workflow and PAML settings, specifically to use the CODEML program. Then, you can try to apply the workflow to analyse your dataset :)
Hope you manage to run CODEML once you have your codon alignment!
All the best,
Sandy