This function writes in a file a tree in parenthetic format using the Newick (also known as New Hampshire) format.
write.tree(phy, file = "", append = FALSE,
digits = 10, tree.names = FALSE)an object of class "phylo" or "multiPhylo".
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 (i.e. the console).
a logical, if TRUE the tree is appended to the file
without erasing the data possibly existing in the file, otherwise
the file (if it exists) is overwritten (FALSE the default).
a numeric giving the number of digits used for printing branch lengths.
either a logical or a vector of mode character. If
TRUE then any tree names will be written prior to the tree on
each line. If character, specifies the name of "phylo"
objects which can be written to the file.
a vector of mode character if file = "", none (invisible
NULL) otherwise.
The node labels and the root edge length, if available, are written in the file.
If tree.names == TRUE then a variant of the Newick format is
written for which the name of a tree precedes the Newick format tree
(parentheses are eventually deleted beforehand). The tree names are
taken from the names attribute if present (they are ignored if
tree.names is a character vector).
The tip labels (and the node labels if present) are checked before being printed: the leading and trailing spaces, and the leading left and trailing right parentheses are deleted; the other spaces are replaced by underscores; the commas, colons, semicolons, and the other parentheses are replaced with dashes.
Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html
Olsen, G. Interpretation of the "Newick's 8:45" tree format standard. http://evolution.genetics.washington.edu/phylip/newick_doc.html