Phylogenetics question

[k-gun12]

This is a bit off-topic but it ties into NGS in that I've got de-novo whole-genome protein predictions from three organisms.. two ingroup and one outgroup taxa. I'm trying to figure out which ingroup taxon is "most like the outgroup" or which ingroup taxon is ancestral. Phylogenetics tells us that there is no "degree of relatedness", just monophyly. How can I tackle this analysis? Presumably if I used phylogenetics I'd just show over and over that the two ingroup taxa are monophyletic but I want to make some assumptions as to similarity to the outgroup. I suppose I could use sheer similarity in the 1:1 orthologs?

Thanks in advance!

[fanx]

I don't understand your question completely. If you really want to see the subtle relatedness among different groups, trees may be not helpful. Instead, you can calculate relative genetic distance at group level between 2 groups. Then, you will see which group is more likely close to your outgroup.