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
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
Hi Daniel,
You may want to try to change the options with phylobase:
phylobase.options(allow.duplicated.labels=ok)
and then try reading your tree.
Feel free to send me your tree if needed.
cheers,
-- François
On Fri, Aug 29, 2014 at 10:42 PM, Daniel Rafael Miranda-Esquivel
Actually, on second thought
length(obj)1
was supposed to be
length(obj)==1
but it turns out not to matter, so you can just use:
readNexus-function(file){
obj-readLines(file)
obj-strsplit(obj[grep(=,obj)], )
obj-sapply(obj,function(x) x[length(x)])
