I have a subset of eukaryotic proteins for which I want to find out from which prokaryotic phylum these proteins originated from. So I blasted these group of proteins against the prokaryotic database and have a set of hits. I grouped the eukaryotic and prokaryotic proteins into protein families using ML and made phylogenetic trees for each family using RaxML. My question is which outgroups can I use to root the phylogenetic trees and whether is it even necessary beyond what is done by default by RaxML? Is drawing conclusions about sister group relationship between eukaryotic and prokaryotic proteins dependent on rooting the trees with proper outgroups?
It sounds like you might be able to draw an inference about the origin of the proteins without rooting the tree, as long as you are willing to assume that the eukaryotic proteins did indeed originate from prokaryotes, rather than, say, the prokaryotes picking up a protein from a eukaryote somehow. Basically, I would look at the point the tree where the (presumably) monophyletic eukaryotic sequences are attached to some group of prokaryotes. That group is the likely sister taxon.
Thank you for clarifying the doubt Andrew. I also think that rooting may not be necessary but wouldn't it help in making more nuanced conclusions though?
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