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consensus trees with branch lengths?

Korbinian Strimmer strimmer at biochem.mpg.de
Sun Nov 21 12:02:20 EST 1999

> We are having an ongoing discussion/disagreement in our lab about
> displaying branch lengths on consensus trees derived from a parsimony
> search, in other words displaying a consensus tree (ie strict consensus)
> as a "phylogram".  Folks in my lab (not me) sent in a manuscript with a
> "consensus phylogram" and the reviewers said not to display a consensus
> tree as a phylogram with no explanation as to what was wrong.

I think there is nothing wrong to display a consensus tree with branch
lengths.  The difficulty is how you actually assign the branch lengths
to the tree topology resulting from the consensus procedure.

I guess what your collegues did is to infer the final branch lengths
from the branch lengths of the underlying trees.  Probably this 
was not convincing to the referees.  An alternative way is to
accept the consensus tree topology as is, and subsequently
assign branch lengths to it using any of the standard methods
(parsimony: Fitch 1971, least-squares: Fitch-Margolish 1967, or 
maximum-likelihood: Felsenstein 1981).


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