Hi,
Ape seems to have a problem with parsing tree names in nexus files.
This can cause problems when using the .nex with other programs.
> library(ape)
> packageVersion("ape")
[1] '3.1.4'
> t <- c(read.tree(text="((a:0.1,b:0.2):0.3,c:0.45);"),
> read.tree(text="((a:0.1,b:0.2):0.3,c:0.55);"))
> names(t) <- c(1, 2)
> write.nexus(t, file="/tmp/t.nex")
> tt <- read.nexus("/tmp/t.nex")
> names(tt)
[1] "\tTREE * 1" "\tTREE * 2"
> write.nexus(tt, file="/tmp/tt.nex")
> ttt <- read.nexus("/tmp/tt.nex")
> names(ttt)
[1] "\tTREE * \tTREE * 1" "\tTREE * \tTREE * 2"
-Graham
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