improvements to compar.gee + bug fix in extract.clade

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

diff --git a/man/read.dna.Rd b/man/read.dna.Rd
index f2f2cff005f461a4c6f992f1e17276007fdac9a3..3f350314155250032c3e5d461a1e4c13567bb337 100644 (file)
--- a/man/read.dna.Rd
+++ b/man/read.dna.Rd
@@ -4,7 +4,7 @@
 \usage{
 read.dna(file, format = "interleaved", skip = 0,
          nlines = 0, comment.char = "#", seq.names = NULL,
-         as.character = FALSE)
+         as.character = FALSE, as.matrix = NULL)
 }
 \arguments{
   \item{file}{a file name specified by either a variable of mode character,
@@ -23,6 +23,12 @@ read.dna(file, format = "interleaved", skip = 0,
     names read in the file are used.}
   \item{as.character}{a logical controlling whether to return the
     sequences as an object of class \code{"DNAbin"} (the default).}
+  \item{as.matrix}{(used if \code{format = "fasta"}) one of the three
+    followings: (i) \code{NULL}: returns the sequences in a matrix if
+    they are of the same length, otherwise in a list; (ii) \code{TRUE}:
+    returns the sequences in a matrix, or stops with an error if they
+    are of different lengths; (iii) \code{FALSE}: always returns the
+    sequences in a list.}
 }
 \description{
   This function reads DNA sequences in a file, and returns a matrix or a
@@ -46,7 +52,7 @@ read.dna(file, format = "interleaved", skip = 0,
   sequential formats, see below). The names of the sequences are read in
   the file unless the `seq.names' option is used. Particularities for
   each format are detailed below.
-  
+
 \itemize{
   \item{Interleaved:}{the function starts to read the sequences when it
     finds 10 contiguous characters belonging to the ambiguity code of
@@ -95,7 +101,7 @@ read.dna(file, format = "interleaved", skip = 0,
   \code{\link{read.GenBank}}, \code{\link{write.dna}},
   \code{\link{DNAbin}}, \code{\link{dist.dna}}, \code{\link{woodmouse}}
 }
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
 \examples{
 ### a small extract from `data(woddmouse)'
 cat("3 40",