write.dna(x, file, format = "interleaved", append = FALSE,
nbcol = 6, colsep = " ", colw = 10, indent = NULL,
blocksep = 1)
"interleaved"
,
"sequential"
, or "fasta"
, or any unambiguous
abbreviation of these.TRUE
the data are appended to the
file without erasing the data possibly existing in the file,
otherwise the file (if it exists) is overwritten (FALSE
the
default).read.dna
and the references below for a description.If the sequences have no names, then they are given "1", "2", ... as names in the file.
With the interleaved and sequential formats, the sequences must be all of the same length. The names of the sequences are not truncated.
The argument `indent' specifies how the rows of nucleotides are
indented. In the interleaved and sequential formats, the rows with
the taxon names are never indented; the subsequent rows are indented
with 10 spaces by default (i.e. if `indent = NULL)'. In the FASTA
format, the rows are not indented by default. This default behaviour
can be modified by specifying a value to `indent': the rows are then
indented with `indent' (if it is a character) or `indent' spaces (if
it is a numeric). For example, specifying `indent = " "' or `indent
= 3' will have exactly the same effect (use `indent = "
The different options are intended to give flexibility in formatting
the sequences. For instance, if the sequences are very long it may be
judicious to remove all the spaces beween columns (colsep = ""), in
the margins (indent = 0), and between the blocks (blocksep = 0) to
produce a smaller file.
The names of the sequences may be truncated with the function
makeLabel
. In particular, Clustal is limited to 30
characters, whereas PHYML seems limited to 99 characters.
The FASTA format may be used as input for Clustal.
Anonymous. IUPAC ambiguity codes.
Felsenstein, J. (1993) Phylip (Phylogeny Inference Package) version
3.5c. Department of Genetics, University of Washington.
read.dna
, read.GenBank
,
makeLabel