Hi Liam and others,
read.nexus() can read NEXUS files that have no TRANSLATE block. There
are two problems with this file: the extra spaces between "begin.../end"
and the semicolon, and the linebreak between the tree declaration and
the Newick string. So the following file can be read by read.nexus:
#NEXUS
begin trees;
tree tagged_tree = [&U] (A,(B,(C,D)60)100);
end;
Best,
Emmanuel
Le 29/08/2014 23:25, Liam J. Revell a écrit :
Hi Daniel.
I think the problem is actually that read.nexus expects a translation
table, and has nothing to do with the labels.
You could use this simplified reading function which does not permit a
translation table & uses phytools read.newick internally:
library(phytools)
readNexus<-function(file){
obj<-readLines(file)
obj<-strsplit(obj[grep("=",obj)]," ")
obj<-sapply(obj,function(x) x[length(x)])
if(length(obj)>1) trees<-read.newick(text=obj)
else {
trees<-lapply(obj,read.newick)
class(trees)<-"multiPhylo"
}
trees
}
Let me know if this works.
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 8/29/2014 4:42 PM, Daniel Rafael Miranda-Esquivel wrote:
Dear all,
I tried to read a tree like this:
#NEXUS
begin trees ;
tree tagged_tree = [&U]
(A,(B,(C,D)60)100);
end ;
using read.nexus; while figtree reads it, ape refuses, telling that
there is an error:
Error in start:end : NA/NaN argument
I tried readNexus in phylobase, but there is a problem reading the
labels (in the real tree, not in this example), as the program
complains that a label is duplicated.
I will be grateful for any tip to solve this problem,
All the best,
Daniel
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