Hi,

I planned to run a DEPS analysis (using the datamonkey server) but noticed that one has to choose one species as the outgroup.  My data set includes representatives of Archaea, Eubacteria, Eukaryotes. The position of the root is uncertain but I would like to try different scenarios, such as placing the root on the branch between Eubacteria and (Archaea, Eukaryotes) etc.

The DEPS program in the downloadable version of the HYPHY package provides the option of the root being unknown (i.e. not available in the online version?) . However, the preferred model of aa evolution (i.e. WAG + F) does not seem to be available for the DEPS analysis in downloaded HYPHY package??

Any suggestion on how to deal with the above situation will be much appreciated. Thanks!

Hi Baci,

DEPS used non time-reversible models, hence where you place the root matters to some extent. The offline version in HYPHY still needs to know which branch to place the root on, the option you are referring to simply allows you to estimate (or not to estimate) WHERE on that branch the root is.

I would suggest you place the root in various points of your tree (as you thought of doing) and try running DEPS on all of them. My guess is, little should change. Some residues may swap roles (i.e. ancestral or derived based on the rooting), but by and large the results will probably remain unchanged.

Sergei