rooting gene trees?

[mkandziora]

Dear Developers,

I just realized, that the README supplied with the 1KP example data, states that gene trees need to be rooted. In the main README, I could not find any information about rooting gene trees or not.

Do we have to supply rooted or unrooted trees?

[smirarab]

Which analysis are you referring to? -m 1 or -m 5 or something else?

[mkandziora]

Ah, it was more a general question, if gene trees need to be rooted or not. Personally, I am interested in the results of the -m 1 method.