Hi Nick & al.
Actually, Nick's method should work too.
If the distance matrix is a patristic distance matrix based on the ML
tree, then neighbor-joining ought to recover the exact topology and
branch lengths of your ML tree. This is on p. 166 of Felsenstein
(2004): "Neighbor-joining, like the least squares methods, is guaranteed
to recover the true tree if the distance matrix happens to be an exact
reflection of a tree."
Maria, are you sure that your distance matrix came from the branch
lengths in your ML tree; and, furthermore, are you sure that NJ did not
give you the correct tree? Keep in mind that NJ will return an unrooted
tree and that the branches might be rotated around any node (thus, your
plotted tree may seem quite different from the ML tree).
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 5/12/2011 5:28 PM, mgavil2 wrote:
Hi Nick,
I tried nj, but the topology I obtain from that is totally different.
I am not sure if it has anything to do with the fact that the tree was
created based on maximum likelihood?
Thanks though!
Meche
On Thu, May 12, 2011 at 4:23 PM, Nick Matzke<mat...@berkeley.edu> wrote:
The APE command NJ (neighbor-joining) will form a tree from a distance
matrix, so that's one option. You could do it and then see if you get the
same topology from NJ as from your topology tree. The branch lengths will
reflect whatever distances were calculated from the data (which might be one
of several corrected or uncorrected distances, depending on the input
sequence/character data).
Cheers,
Nick
On 5/12/11 2:18 PM, mgavil2 wrote:
All,
I have a tree topology (tree_name.tre), and a distance matrix, based
on that tree topology. However I cant not seem to find the nexus file
from which the matrix was generated. Is there a way to use that
distance matrix to incorporate branch lengths into my topology?
I have looked into all the threads of questions posted in the list,
but still can not find an answer. my final objective is just to
generate a tree with branch lengths proportional to the distances on
the matrix (reviewers requirement for a publication).
Any suggestions would be greatly appreciated!
Thanks.
Maria Mercedes
--
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
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Dept. personal page:
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Lab phone: 510-643-6299
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Cell phone: 510-301-0179
Email: mat...@berkeley.edu
Mailing address:
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3060 VLSB #3140
Berkeley, CA 94720-3140
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thought the earth was spherical, they were wrong. But if you think that
thinking the earth is spherical is just as wrong as thinking the earth is
flat, then your view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer,
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