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!