}
\description{
This function writes in a file a list of DNA sequences in sequential,
- interleaved, or FASTA format. The names of the vectors of the list are
- used as taxa names.
+ interleaved, or FASTA format.
}
\details{
- The same three formats are supported in the present function than in
- \code{\link{read.dna}}: see its help page and the references below for
- a description of these formats.
+ Three formats are supported in the present function: see the help page
+ of \code{\link{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; if the taxon names are longer than 10 characters,
- they are truncated and a warning message is issued.
+ of the same length. The names of the sequences are not truncated.
- The argument `indent' specifies how the rows of nucleotides are
+ The argument \code{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
+ with 10 spaces by default (i.e., if \code{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 = "\t"' for a
- tabulation).
+ can be modified by specifying a value to \code{indent}: the rows are then
+ indented with ``indent'' (if it is a character) or `indent' spaces (if
+ it is a numeric). For example, specifying \code{indent = " "} or
+ \code{indent = 3} will have the same effect (use \code{indent = "\\t"}
+ for a tabulation).
+
+ 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.
}
\note{
Specifying a negative value for `nbcol' (meaning that the nucleotides
are printed on a single line) gives the same result for the
interleaved and sequential formats.
- 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
+ \code{\link{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.
}
\value{
None (invisible `NULL').
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\references{
Anonymous. FASTA format description.
\url{http://www.ncbi.nlm.nih.gov/BLAST/fasta.html}
\url{http://evolution.genetics.washington.edu/phylip/phylip.html}
}
\seealso{
- \code{\link{read.dna}}, \code{\link{read.GenBank}}
+ \code{\link{read.dna}}, \code{\link{read.GenBank}},
+ \code{\link{makeLabel}}
}
\keyword{IO}