Target tree in TreeAnnotator
Kokshoorn, B.
Dear All,
I created two consensus trees of a set of 10,000 trees by using PAUP* and TreeAnnotator. The trees differed in both support values (posteriors) and topology. So I tried to use the PAUP* consensus as a target tree in TreeAnnotator to see what support that gives.
Here comes my problem; TreeAnnotator keeps telling me there is something wrong with the syntax of the target tree (which was direct PAUP* output). So i fiddeled around with it, but no solution yet.
Might it have something to do with the target tree being rooted or not?
Any suggestions?
Thanks in advance!
Cheers, Bas Kokshoorn.
Leiden University, The Netherlands.
alexei....@gmail.com
must be a bifurcation). I think that PAUP* will produce a consensus
tree with a trifurcation at the root. This could be your problem.
Alexei
Andrew Rambaut
TreeAnnotator doesn't create a consensus tree. It finds the tree in
your posterior sample (the trees file) that
has the highest sum of posterior probabilities for all the clades in
the tree. The point is that this is an actual
tree that BEAST visited. It can also be used to annotate a specific
tree but this is expected to be a tree from
BEAST (such as a random tree from the chain). Consensus trees will
have polytomies or unresolved nodes and these
cannot be read by TreeAnnotator. I can't see a sensible way of
finding HPD or mean age for an unresolved node
(polytomy) so there is no reason to use consensus trees in
TreeAnnotator (unless they are fully resolved and
rooted).
Andrew
Geoff Nicholls
A modal tree is going to be good summary statistic when the posterior
dbn is concentrated
on a small set of trees. If you want a compact representation of the
uncertainty in
tree topology, the consensus network approach is nice. It is implemented
in SplitsTree4. You load the MCMC output trees, and generate a network
in which shows splits supported above a threshold, which you set.
It is unrooted. As far as I know there is no notion of a rooted
consensus net.
Geoff