X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fclustal.Rd;h=afb8d735c2cff167bd267fba5c336f291054e18d;hb=dfe58641d0e6fe53612710cd92401306273609f4;hp=8bb5cfbe3d0352fc0d3e487c26bfd2d61ca63127;hpb=453ad4ce9e573998f28185d92c8d71367dd32f23;p=ape.git

diff --git a/man/clustal.Rd b/man/clustal.Rd
index 8bb5cfb..afb8d73 100644
--- a/man/clustal.Rd
+++ b/man/clustal.Rd
@@ -10,9 +10,11 @@
 \usage{
 clustal(x, pw.gapopen = 10, pw.gapext = 0.1,
         gapopen = 10, gapext = 0.2, exec = NULL,
-        MoreArgs = "", quiet = TRUE)
-muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
-tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
+        MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
+muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE,
+       original.ordering = TRUE)
+tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE,
+        original.ordering = TRUE)
 }
 \arguments{
   \item{x}{an object of class \code{"DNAbin"}.}
@@ -25,6 +27,8 @@ tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
   \item{MoreArgs}{a character string giving additional options.}
   \item{quiet}{a logical: the default is to not print on \R's console the
     messages from the external program.}
+  \item{original.ordering}{a logical specifying whether to return the
+    aligned sequences in the same order than in \code{x}.}
 }
 \details{
   \code{clustal} tries to guess the name of the executable program
@@ -48,24 +52,21 @@ tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
   Higgins, D. G. and Thompson, J. D. (2003) Multiple sequence alignment
   with the Clustal series of programs. \emph{Nucleic Acids Research}
   \bold{31}, 3497--3500.
-
   \url{http://www.clustal.org/}
 
   Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high
   accuracy and high throughput. \emph{Nucleic Acids Research},
   \bold{32}, 1792--1797.
-
   \url{http://www.drive5.com/muscle/muscle_userguide3.8.html}
 
   Notredame, C., Higgins, D. and Heringa, J. (2000) T-Coffee: A novel
   method for multiple sequence alignments. \emph{Journal of Molecular
   Biology}, \bold{302}, 205--217.
-
   \url{http://www.tcoffee.org/Documentation/t_coffee/t_coffee_technical.htm}
 }
 \author{Emmanuel Paradis}
 \seealso{
-  \code{\link{image.DNAbin}}, \code{\link{del.gaps}}
+  \code{\link{image.DNAbin}}, \code{\link{del.gaps}}, \code{\link{alex}}
 
   The package \pkg{phyloch} which has similar functions for the MAFFT
   and Prank.