These functions call their respective program from R to align a set of
nucleotide sequences of class
"DNAbin". The application(s) must
be installed seperately and it is highly recommended to do this so
that the executables are in a directory located on the PATH of the
1 2 3 4 5 6 7 8
clustal(x, pw.gapopen = 10, pw.gapext = 0.1, gapopen = 10, gapext = 0.2, exec = NULL, MoreArgs = "", quiet = TRUE, original.ordering = TRUE) clustalomega(x, exec = NULL, MoreArgs = "", quiet = TRUE) muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE, original.ordering = TRUE) tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
an object of class
gap opening and gap extension penalties used by Clustal during pairwise alignments.
idem for global alignment.
a character string giving the name of the program, with
its path if necessary.
a character string giving additional options.
a logical: the default is to not print on R's console the messages from the external program.
a logical specifying whether to return the
aligned sequences in the same order than in
It is highly recommended to install the executables properly so that
they are in a directory located on the PATH (i.e., accessible from any
other directory). Alternatively, the full path to the executable
may be given (e.g.,
exec = "~/muscle/muscle"), or a (symbolic)
link may be copied in the working directory. For Debian and its
derivatives (e.g., Ubuntu), it is recommended to use the binaries
distributed by Debian.
clustal tries to guess the name of the executable program
depending on the operating system. Specifically, the followings are
used: “clustalw” under Linux, “clustalw2” under MacOS, or
“clustalw2.exe” under Windows.
clustalomega, “clustalo[.exe]” is the default on all
systems (with no specific path) since it seems there is no Windows
The computations are done in a temporary directory which is deleted
when R is quit. So it is possible to find the files created by the
last call in the directory printed by
When called without arguments (i.e.,
clustal(), ...), the
function prints the options of the program which may be passed to
an object of class
"DNAbin" with the aligned sequences.
clustalomega is actually for AA sequences only.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G. and Thompson, J. D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research 31, 3497–3500. http://www.clustal.org/
Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797. 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. Journal of Molecular Biology, 302, 205–217. http://www.tcoffee.org/
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., S\"oding, J., Thompson, J. D. and Higgins, D. G. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7, 539.
1 2 3 4 5 6 7 8 9 10 11 12 13
## Not run: ### display the options: clustal() muscle() tcoffee() data(woodmouse) ### open gaps more easily: clustal(woodmouse, pw.gapopen = 1, pw.gapext = 1) ### T-Coffee requires negative values (quite slow; muscle is much faster): tcoffee(woodmouse, MoreArgs = "-gapopen=-10 -gapext=-2") ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.