I have a couple of questions regarding obtaining dn/ds values for a gene family within a species using codeml. In my case, I have 67 genes and hoping to calculate dn/ds for each gene (not site) to identify which genes are under selection. Most of the tutorials and papers I read talk about genes belong to multiple spp. So I would appreciate it if someone can help me to come up with the ideal setting to run codeml for this specific scenario. I already have codon aligned seq alignment and ML tree (protein) of the genes of interest. I use PAML4.9j on pamIX frontend. Thanks in advance.