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
>
>
>
>
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