5 \title{Multiple Sequence Alignment with External Applications}
7 These functions call their respective program from \R to align a set of
8 nucleotide sequences of class \code{"DNAbin"}.
11 clustal(x, pw.gapopen = 10, pw.gapext = 0.1,
12 gapopen = 10, gapext = 0.2, exec = NULL,
13 MoreArgs = "", quiet = TRUE)
14 muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
15 tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
18 \item{x}{an object of class \code{"DNAbin"}.}
19 \item{pw.gapopen, pw.gapext}{gap opening and gap extension penalties
20 used by Clustal during pairwise alignments.}
21 \item{gapopen, gapext}{idem for global alignment.}
22 \item{exec}{a character string giving the name of the program, with
23 its path if necessary. \code{clustal} tries to guess it depending on
24 the operating system (see details).}
25 \item{MoreArgs}{a character string giving additional options.}
26 \item{quiet}{a logical: the default is to not print on \R's console the
27 messages from the external program.}
30 \code{clustal} tries to guess the name of the executable program
31 depending on the operating system. Specifically, the followings are
32 used: ``clustalw'' under Linux, ``clustalw2'' under MacOS, or
33 ``C:/Program Files/ClustalW2/clustalw2'' under Windows.
35 The calculations are done in a temporary directory which is deleted
36 when \R is quit. So it is possible to find the files created by the
37 last call in the directory printed by \code{tempdir()}.
39 When called without arguments (i.e., \code{clustal()}, \dots), the
40 function prints the options of the program which may be passed to
44 an object of class \code{"DNAbin"} with the aligned sequences.
47 Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J.,
48 Higgins, D. G. and Thompson, J. D. (2003) Multiple sequence alignment
49 with the Clustal series of programs. \emph{Nucleic Acids Research}
50 \bold{31}, 3497--3500.
51 \url{http://www.clustal.org/}
53 Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high
54 accuracy and high throughput. \emph{Nucleic Acids Research},
55 \bold{32}, 1792--1797.
56 \url{http://www.drive5.com/muscle/muscle_userguide3.8.html}
58 Notredame, C., Higgins, D. and Heringa, J. (2000) T-Coffee: A novel
59 method for multiple sequence alignments. \emph{Journal of Molecular
60 Biology}, \bold{302}, 205--217.
61 \url{http://www.tcoffee.org/Documentation/t_coffee/t_coffee_technical.htm}
63 \author{Emmanuel Paradis}
65 \code{\link{image.DNAbin}}, \code{\link{del.gaps}}, \code{\link{alex}}
67 The package \pkg{phyloch} which has similar functions for the MAFFT
72 ### display the options:
78 ### open gaps more easily:
79 clustal(woodmouse, pw.gapopen = 1, pw.gapext = 1)
80 ### T-Coffee requires negative values (quite slow; muscle is much faster):
81 tcoffee(woodmouse, MoreArgs = "-gapopen=-10 -gapext=-2")