some news for ape 3.0-8

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

diff --git a/man/write.dna.Rd b/man/write.dna.Rd
index 8a692f1491993badbe70231d20f47f2e87c1a716..2ff245da3af4a9252e73c6cc734a97f8df16e682 100644 (file)
--- a/man/write.dna.Rd
+++ b/man/write.dna.Rd
@@ -45,16 +45,16 @@ write.dna(x, file, format = "interleaved", append = FALSE,
   With the interleaved and sequential formats, the sequences must be all
   of the same length. The names of the sequences are not truncated.
 
   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
+  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
 
   The different options are intended to give flexibility in formatting
   the sequences. For instance, if the sequences are very long it may be


@@ -64,19 +64,17 @@ write.dna(x, file, format = "interleaved", append = FALSE,
 }
 \note{
   Specifying a negative value for `nbcol' (meaning that the nucleotides
 }
 \note{
   Specifying a negative value for `nbcol' (meaning that the nucleotides

-  are printed on a single line) gives the same result for the
+  are printed on a single line) gives the same output for the

   interleaved and sequential formats.
 
   The names of the sequences may be truncated with the function
   \code{\link{makeLabel}}. In particular, Clustal is limited to 30
   interleaved and sequential formats.
 
   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.
+  characters, and PHYML seems limited to 99 characters.

 }
 \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}