Hi all, I am testing the liklihood of various possible trees using phylip or paml. Each time I do this I am aligning one relatively short sequence of interest against a large alignment of mitochondrial genomes. I already have aligned the mitochondrial genomes, so each time this process is run I just want to align my sequence against this pre-made alignment.
How can I do this? I think I've heard about this kind of thing being done but searching now can't find any reference to it whatsoever. Thanks, Harry