Hi Annemarie.
To estimate branch lengths on a fixed topology you might want to try
acctran for MP edge lengths; and optim.pml(...,optEdge=TRUE) (with all
other options FALSE) for ML. Both of these functions are in the phangorn
package. Look at the phangorn vignette "Ancestral sequence
Reconstruction"
(http://cran.r-project.org/web/packages/phangorn/index.html) for details.
- 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 4/30/2012 11:36 AM, Annemarie Verkerk wrote:
Dear R-sig-phylo users,
I have a question about generating branch lengths on an existing tree
topology that has no branch length. I would like to compute branch
lengths on a tree topology of 20 taxa, preferably using something like
parsimony or maximum compatibility. I guess this problem equals a
phylogenetic tree estimation while restricting the phylogeny to have a
specific set of internal nodes / bipartitions. I've been told to use
PAUP, but I don't know anything about PAUP and I feel there must be a
way to do this in R!
I've tried the nnls.tree() method available in the phangorn package, but
with my dataset, most of the internal edges were estimated to be zero,
effectively reducing my existing topology to a star phylogeny. I am
going to try it again with another dataset, but I would like to compare
the results of generating the branch lengths on both datasets. Is there
any other way to do this in R?
Your feedback is much appreciated!
Many thanks,
Annemarie
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