write.tree {ape} | R Documentation

## 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.

### 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).

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.

### Value

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

### Author(s)

Emmanuel Paradis, Daniel Lawson dan.lawson@bristol.ac.uk, and Klaus Schliep kschliep@snv.jussieu.fr

### 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

### See Also

`read.tree`, `read.nexus`, `write.nexus`

[Package ape version 5.1 Index]