This function writes trees in a file with the NEXUS format.
write.nexus(..., file = "", translate = TRUE, digits = 10)None (invisible `NULL').
either (i) a single object of class "phylo", (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects.
a file name specified by either a variable of mode character,
or a double-quoted string; if file = "" (the default) then the
tree is written on the standard output connection.
a logical, if TRUE (the default) a translation
of the tip labels is done which are replaced in the parenthetic
representation with tokens.
a numeric giving the number of digits used for printing branch lengths. For negative numbers no branch lengths are printed.
Emmanuel Paradis
If several trees are given, they must all have the same tip labels.
If among the objects given some are not trees of class "phylo",
they are simply skipped and not written in the file.
See write.tree for details on how tip (and node) labels
are checked before being printed.
Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590--621.
read.nexus, read.tree,
write.tree, read.nexus.data,
write.nexus.data, write.phyloXML