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Rooted tree/ any comments?

R M Bernstein ralph at ccit.arizona.edu
Sat Nov 4 21:26:14 EST 1995


In Article <47f0na$eqe at nntp3.u.washington.edu>,
joe at evolution.genetics.washington.edu (Joe Felsenstein) wrote:

>Are you inferring rooted or unrooted trees?  From the picture, rooted.
>But parsimony, likelihood, and most distance matrix methods (such as
>Neighbor-Joining or Fitch-Margoliash) do _not_ estimate rooted trees.
>They estimate unrooted trees.  And for three taxa there is only one possible
>unrooted tree, so all methods will give the same tree, which is always the
>right one, but the whole matter is therefore vacuous.
>
>I can only interpret your posting as based on the total misconception
>that distance matrix methods infer rooted trees and do so by clustering
>algorithms, which put the closest pair together and then put the root
>below that. 
>
>-----
>Joe Felsenstein         joe at genetics.washington.edu     (IP No. 128.95.12.41)
> Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

To Joe and other tree people,
How can you root a tree when a divergent gene is unknown?
For ex, in immunoglobulins, no one knows what would be a good
V-region "root" for v-region tree. Some say thy-1 , but its a shaky 
v-region relative at best. I work on the evolution the immune system,
and am thinking of how to make a rooted tree with a new class of ig that
i recently cloned.  I dont know if it is the "oldest" ig or if one or
several of its domains are older than the others.  I make CLUSTALW
trees using NJ but would really like to do a rooted tree.  Any suggestion?

Regards, Ralph


Ralph M. Bernstein
Dept of Micro/Immuno
University of Arizona
Ph: 602 626 2585
Fx: 602 626 2100
url: http://lamprey.medmicro.arizona.edu
     http://radon.gas.uug.arizona.edu/~bernster



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