Hi Luigi.
Unfortunately, I think you may need to supply us with some more details
to try and figure out what your problem is.
Does your code look like:
D<-dist.dna(obj)
## obj is class "DNAbin", e.g.:
## data(woodmouse)
## obj<-woodmouse
tree<-upgma(D)
plot(tree) ## works
write.nexus(tree,file="filename.nex") ## does not work?
If so, I was able to get this to run on test datasets without a problem.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 12/27/2014 6:57 PM, Luigi Marongiu wrote:
Dear Liam,
I ran in a similar problem as the one posed by Elaine, but when I used
the argument file = "filename.nex" I still obtained "Error in
y$tip.label : $ operator is invalid for atomic vectors".
To be clear I aligned the sequences using muscle(), created a distance
matrix using dist.dna(), computed the tree using upgma() and now I would
like to save the tree using nexus().
Any tip?
regards
Luigi
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