Hi Robin.
Yes, you can do this under the ACCTRAN (accelerated transformation)
criterion using the function acctran() in "phangorn." To do this given
a data file "sequences.dna" in FASTA format:
> dna<-read.phyDat("sequences.dna",format="fasta")
> tree<-pratchet(dna) # or you could use optim.parsimony()
> tree<-acctran(tree,dna)
I hope this helps.
- 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 9/2/2011 8:35 AM, Velzen, Robin van wrote:
Dear R-sig phylo list members,
I am trying to apply maximum Parsimony tree searches on a large number of
simulated datasets within the R environment. So far I have found one function
implementing Parsimony: the optim.parsimony function in the package phangorn.
This function finds a shortest tree for a typical dataset (1000 taxa)
reasonably fast which is great. However, the resulting tree does not include
branch lengths (i.e. it is a fully bifurcating cladogram). This is problematic
for me because there are nodes separating identical sequences.
Is there a way (i.e. function) to calculate branch lengths in terms of number
of substitutions for a tree?
..Or does someone know an alternative function to get a maximum Parsinomy tree
with branch lengths?
Any help or suggestion would be most welcome.
Thanks!
Robin
Robin van Velzen
Biosystematics Group
Wageningen University
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