write.nexus: Write Tree File in Nexus Format

In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description

This function writes trees in a file with the NEXUS format.

Usage

write.nexus(..., file = "", translate = TRUE, original.data = TRUE)

Arguments

...	either (i) a single object of class "phylo", (ii) a series of such objects separated by commas, or (iii) a list containing such objects.
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.
translate	a logical, if TRUE (the default) a translation of the tip labels is done which are replaced in the parenthetic representation with tokens.
original.data	a logical, if TRUE (the default) the data in the original NEXUS file are eventually written in "file" (see below).

Details

If original.data = TRUE, the file as specified by the attribute "origin" of the first tree is read and its data (except the trees) are written in file.

If several trees are given, they must have all the same tip labels.

If among the objects given some are not trees of class "phylo", they are simply skipped and not written to the file.

Value

None (invisible ‘NULL’).

Author(s)

Emmanuel Paradis

References

Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590–621.

See Also

read.nexus, read.tree, write.tree, read.nexus.data, write.nexus.data

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.