I want to test selection acting on one gene (set as my foreground) compared to a duplicate of the same gene (leaving it as background) but I'm not sure how to set up my files. I have alignments for the two genes, but this means I have to combine them into one alignment file. This means that all my species will have duplicated names. if I change the duplicated names then my one species tree won't work because half the sequences' names won't be detected.
I tried producing a tree with the combined MSA and it ended up looking like a smaller tree (for one gene)embedded in the middle of another tree for the second gene. I have no idea how I could unroot it like this...
Concatenating the dataset also does not make sense to me since I'd want to specifically make two partitions, one for each gene. Or is there another way to test for selection strength for duplicated genes?
Could you please clarify what "my one species tree won't work" means?
In PAML you typically run one alignment file and one treefile where the species names in the alignment have to exist and match exactly to the names in the treefile. So if I want to double my alignment by adding a gene, I'd have to attach something to the second set of species names like "sp1-2", "sp2-2" otherwise duplicated names can cause a problem (at least it did when I ran it in different models on datamonkey). Now...by changing the second set of names, they no longer "exist" in the treefile. So it's just this weird loop of problems. Simply concatenating the second gene alignment to my first gene alignment doesn't help since I wanted to label the second gene as a foreground.