Re: PhyloCode Discussion: Crowns, Panstems, and their Correspondence to each oth

[David Marjanovic <david.marjanovic@gmx.at>]

> Ah, but have you determined how to make stepmatrices work correctly in
PAUP
> yet?  You'll recall our attempts resulted in trees rooted on incorrect
taxa,

Yes -- that's because a stepmatrix fixes the plesiomorphic state for that
character, and this way polarizes the entire tree. It roots the entire tree.
For making a rooted tree, PAUP* includes the ancestor "standard" in the
analysis. It is coded ? for _all_ characters; this is why I always got my
trees rooted on *Alexornis* before I made up an ancestor myself and coded it
0 for all characters. This correctly rooted the tree on the equally
artificial allzero outgroup.

> and amazingly small numbers of MPT's.

Really? I got stupendously high numbers of MPTs. Tens of thousands for 62
characters and 43 taxa or suchlike. When I excluded the taxa with less than
10 codings, I even got over 140,000 MPTs.