bunch of fixes for ape 3.0-2

[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,
 }
 \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{
 }
 \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
 
   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
   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
   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.
 
 }
 \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').
 }
 }
 \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}
 \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{
   \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}
 }
 \keyword{IO}