It looks like the NEXUS file might be badly conformed.
You could try:
obj<-scan(file="TimetreeOfLife2015.tre",n=1,skip=2,what="character")
tree<-read.tree(text=obj)
That seemed to work for me.
- Liam
Liam J. Revell, Associate 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 5/23/2016 12:11 PM, Sergio Ferreira Cardoso wrote:
Dear all,
I am trying to open a .tre file with ape. I downloaded the tree from
http://www.timetree.org/book#treefiles. It's a .tre (not .nex) file, but
it's essentially a nexus. I tried to open it:
tr <- read.nexus(file="TimetreeOfLife2015.tre")
Error in trees[[i]] : subscript out of bounds
I tried to change the file name to .nex, but it wouldn't work. I saw some
previous threads but I couldn't solve the problem.
Does anyone know how can I solve this?
Thanks in advance,
Sérgio.
ps: I have the lastest 3.4 version of ape.
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