I have a mtDNA data set with 3 different genes with different translation frames.  I don't really want to partition the data set into 3 partitions for each of the 3 genes but rather set the translation frame for each gene, and only have one phylogenetic tree. I am looking at dn/Ds ratios and when I partition it into 3 genes, and optimize the likelihood I get synonymous and nonsynonymous omegas for each partition.  Can I set the translation frame for each gene without creating different partitions? thanks