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

Hi Steve,

For your setup the simplest approach would be to concatenate the three genes (in appropriate reading frames) into a single partition before feeding them into HyPhy (e.g. through the GUI or standard analyses). Alternatively, you can start with three genes as separate partitions, and then constrain partition-wide parameters to be the same.

How are you trying to do it currently (e.g. GUI)?

Sergei