Dear Joe, Thanks for your feedback on this question. I will go read those pages you mentioned.
Scott On Wed, Nov 21, 2012 at 5:19 PM, Joe Felsenstein <j...@gs.washington.edu>wrote: > > Daniel Barker wrote: > > What should branch lengths on a consensus tree represent? > > Scott Chamberlain had written: > > > When making a consensus tree using ape::consensus the branch lengths are > > lost. Is there a way to not lose the branch lengths? Or to add them > > somehow > > to the consensus tree after making it. > > > The issue of what branch lengths ought to be on a consensus tree is not > simple. If we have three rooted trees: > ((A:1,B:1):1,C:2); > ((A:1,B:1):1,C:2); > (A:2,(B:1,C:1):1); > > the consensus tree should be the first tree, but what branch length should > be used for (say) the branch ancestral to the AB clade? 1? 0.667? > > The minute you open this can of worms it becomes clear that the answer > depends on what you want that number to convey and what interpretations > your audience will tend to draw from the number. There is no "obvious" > answer. So this is not a mere technical computing question. > > By the way, in my 2004 book, you will find me agonizing about this on page > 526, coming down on the side of 0.667, but not overwhelmingly convincingly. > You could argue that a branch length should be set 0 when the branch is > not there, and all the resulting values averaged, or you could argue that > the average should only be taken over those trees for which that branch is > present. > > One possible way to solve the problem is to take the consensus tree as if > it were a user-defined tree, use your whole data set, and infer branch > lengths on that tree. Daniel has already expressed his legitimate concerns > in such a case as to whether it takes (for example) trifurcations as if > they were real rather than an expression of our uncertainty. > > J.F. > ---- > Joe Felsenstein j...@gs.washington.edu > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > > (from 1 October 2012 to 10 December 2012 on sabbatical leave at) > Department of Statistics, University of California, Berkeley, 367 Evans > Hall, Berkeley, CA 94710 > > > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo