I am a beginner to Dendropy and am struggling with a relatively simple task.
I have a big unrooted Newick file containing data on the tree of life. I would like play around with rooting this tree in various ways.
For example, the first thing I want to try is to root the tree such that one branch contains all of the bacteria (and nothing else), while the other branch leads to the common ancestor of archaea and eukaryotes. (So from that node, one branch should lead to all the eukaryotes and the other should lead to all of the archaea.)
I can easily identify which taxa are in which domain from their labels. The problem is that Tree.mrca doesn't seem to work for getting the last common ancestor of all the eukaryotes (or bacteria etc.). It chooses a node that is a common ancestor of the eukaryotes but also includes some other taxa as well. This makes sense, because "most recent" doesn't really make sense for an unrooted tree.
But on the other hand it seems like it should be possible to root the tree in this way, from the data that I have. There is one unique edge in the tree that has all the bacteria on one side and everything else on the other, and I just need a way to find that edge. Is there a way this can be accomplished in dendropy?