I've been battling with codes and it's no use. There must be a way to select a group of taxa as the outgroup, but I couldn't find how.
I suppose that the alternative path is to make the whole analysis and constraint that group as a family.
Any thoughts on how to resolve this?
To the best of my knowledge, that's the way to go.
You could force the monophyly of the ingroup, and then select the outgroup taxon (which will be with the rest of the excluded taxa). Remember that in the search settings window, you must activate the enforce constraints for them to apply.
Constrain it as a family only if you are sure, from previous work, that none belong within the group that you consider the in-group. Otherwise you are setting the analysis up to find the best tree that fits your constraint rather than the globally best tree.
Remember that tree inference itself renders an unrooted tree always. To do anything else is currently beyond the ability of the best computers: far too many ways to root a tree for the computer to ever finish a run.
The rooting always depends on what you know, apriori, about the comparative biological histories of the outgroup to the in-group (the group of interest).
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