write.tree: Write Tree File in Parenthetic Format

Description

This function writes in a file a tree in parenthetic format using the Newick (also known as New Hampshire) format.

Usage

write.tree(phy, file = "", append = FALSE, digits = 10, tree.names = FALSE)

Arguments

phy

an object of class "phylo" or "multiPhylo".

file

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).

append

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).

digits

a numeric giving the number of digits used for printing branch lengths.

tree.names

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.

Value

a vector of mode character if file = "", none (invisible NULL) otherwise.

Details

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).

References

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