Hi Liam,
thanks, the acctran() function worked for me! I'm sorry I did not
realize this question was already asked and answered here, I did not
find that on google at first (for future reference):
http://www.mail-archive.com/[email protected]/msg01734.html
Many thanks!
Regards,
Annemarie
Liam J. Revell wrote:
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
--
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
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