write.nexus.data {ape} | R Documentation |
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.
write.nexus.data(x, file, format = "dna", datablock = TRUE, interleaved = TRUE, charsperline = NULL, gap = NULL, missing = NULL)
x |
a matrix or a list of sequences each made of a single vector of mode character where each element is a character state (e.g., “A”, “C”, ...) Objects of class of “DNAbin” are accepted. |
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” (the default) or “protein”, or any unambiguous abbreviation of these (case insensitive). |
datablock |
a logical, if |
interleaved |
a logical, if |
charsperline |
a numeric specifying the number of characters per
line when used with |
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.
Default symbols for missing data and gaps can be changed by using the
missing
and gap
commands.
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: ## Write interleaved DNA data with 100 characters per line in a DATA block data(woodmouse) write.nexus.data(woodmouse, file= "wood.ex.nex", interleaved = TRUE, charsperline = 100) ## Write sequential DNA data in TAXA and CHARACTERS blocks data(cynipids) write.nexus.data(cynipids, file = "cyn.ex.nex", format = "protein", datablock = FALSE, interleaved = FALSE) unlink(c("wood.ex.nex", "cyn.ex.nex")) ## End(Not run)