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
--
Annemarie Verkerk, MA
Evolutionary Processes in Language and Culture (PhD student)
Max Planck Institute for Psycholinguistics
P.O. Box 310, 6500AH Nijmegen, The Netherlands
+31 (0)24 3521 185
http://www.mpi.nl/research/research-projects/evolutionary-processes
_______________________________________________
R-sig-phylo mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
