I am trying to calculate dn/ds ratio for several genes. I am trying to analyze the selection pressure on several bacterial genes. I have 12 bacterial genomes and 1600 gene clusters i.e. gene1 in all 12 species and gene2 in all 12 species and so on.. I would like to calculate dn/ds for all genes. I tried KaKs calculator, R script and other tools but all are for pair of sequences only. Any suggestion will be deeply appreciated.