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/
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Lab personal page:
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Email: mat...@berkeley.edu
Mailing address:
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3060 VLSB #3140
Berkeley, CA 94720-3140
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"[W]hen people thought the earth was flat, they were wrong.
When people 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, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
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