bug fix in mcmc.popsize()

[ape.git] / man / write.dna.Rd

diff --git a/man/write.dna.Rd b/man/write.dna.Rd
index 3646ef9664255cb14a5d456115bff13593b08f00..fb87ae71e8f5b2be5f63dbff78cf1fba013e1a1d 100644 (file)
--- a/man/write.dna.Rd
+++ b/man/write.dna.Rd
@@ -33,47 +33,50 @@ write.dna(x, file, format = "interleaved", append = FALSE,
 }
 \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}
@@ -86,6 +89,7 @@ write.dna(x, file, format = "interleaved", append = FALSE,
   \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}