I was wondering if you all had any program besides BEAST (which I am excluding for pipeline reasons, for now) that allows you to estimate a tree that includes a known ancestral state and a known topology? For instance, a simple 3 taxa example where one taxa (A) is ancestral to the other two (B,C) (and thus, the topology is fixed) but where there is another common ancestor (D) that comes later that is younger than (A) but older than (B,C) that I would like to infer the ancestral states if? Particularly working with DNA sequencing data (a concatenated alignment).
So somewhat like this:
-----B | A---D | -----------C
Where I know the sequences A, B, and C and want to infer D (for all DNA sites). Bonus points if it can actually do the branch lengths at the same time.
BEAST is a bit overkill and hard to pipeline (as you must, as I understand it, define the ancestral states a priori which could be a problem for me down the road).
Any tips or direction would be appreciated, Best!