write.nexus.data: Write Character Data In NEXUS Format
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function writes in a file a list of sequences in the NEXUS format.The names of the vectors of the list are used as taxon names.

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write.nexus.data(x, file, format = "dna", datablock = TRUE,
                 interleaved = TRUE, charsperline = NULL,
                 gap = NULL, missing = NULL)

`x`	a list of sequences each made of a single vector of mode character where each element is a character state (e.g. “A”, “C”, ...).
`file`	a file name specified by either a variable of mode character, or a double-quoted string.
`format`	a character string specifying the format of the sequences. Two choices are possible: `dna`, or `protein`, or any unambiguous abbreviation of these. Default is “`dna`”.
`datablock`	a logical, if `TRUE` the data are written in a single DATA block. If `FALSE` data is written in TAXA and CHARACTER blocks. Default is `TRUE`.
`interleaved`	a logical, if `TRUE` the data is written in interleaved format with number of characters per line as specified with `charsperline = numerical_value`. If `FALSE`, data is written in sequential format. Default is `TRUE`.
`charsperline`	a numeric specifying the number of characters per line when used with `interleaved = TRUE`. Default is `80`.
`gap`	a character specifying the symbol for gap. Default is “`-`”.
`missing`	a character specifying the symbol for missing data. Default is “`?`”.

If the sequences have no names, then they are given “1”, “2”, ..., as names in the file.

Sequences must be all of the same length (i.e., aligned).

Default symbols for missing data and gaps can be changed by using the missing and gap commands.

Please see files ‘data.nex’ and ‘taxacharacters.nex’ for examples of output formats.

None (invisible ‘NULL’).

...

Johan Nylander nylander@scs.fsu.edu

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,write.nexus, read.nexus.data

## Not run: \dontshow{library(ape)}
## Write interleaved DNA data with 100 characters per line in a DATA block
## Not run: data("woodmouse")
## Not run: write.nexus.data(woodmouse, file= "woodmouse.example.nex", interleaved = TRUE, charsperline = 100)
## Write sequential DNA data in TAXA and CHARACTERS blocks
## Not run: data("cynipids")
## Not run: write.nexus.data(cynipids, file= "cynipids.example.nex", format = "protein", datablock = FALSE, interleaved = FALSE)
## Not run: \dontshow{unlink(c("woodmouse.example.nex", "cynipids.example.nex"))}