How should I analyze a gene family that does not exist in the outgroup?

[Eika728]

Hi Ben,
I'm a new user of CAFE, and during my first run I didn’t filter out gene families that have zero copies in the outgroup. Based on that initial analysis, I found a very interesting gene family.

However, I later realized that this family has no copies in my outgroup species (probably because the outgroup I chose is quite distantly related, and this family might be specific to the clade I’m studying).

I’d like to ask: Could this make the analysis for this family unreliable, meaning I should probably remove it from my CAFE input file? Since this family is really interesting, I don’t want to drop it from my analysis. T T

Thank you!

[hahnlab-user]

Hello,

CAFE doesn't really think in terms of "outgroups," though it does assume that the families you are studying exist at the root of your tree: families can't be created on a later branch. As a consequence, if families don't exist in what you're calling your outgroup, CAFE will infer that they were lost along that branch. So if you can live with that (or ignore that inferred loss) there's no problem. Alternatively, just do the analysis without the outgroup--CAFE doesn't mind!

Matt