clustal {ape} | R Documentation |
These functions call their respective program from R to align a set of
nucleotide sequences of class "DNAbin"
.
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)
x |
an object of class |
pw.gapopen, pw.gapext |
gap opening and gap extension penalties used by Clustal during pairwise alignments. |
gapopen, gapext |
idem for global alignment. |
exec |
a character string giving the name of the program, with
its path if necessary. |
MoreArgs |
a character string giving additional options. |
quiet |
a logical: the default is to not print on R's console the messages from the external program. |
original.ordering |
a logical specifying whether to return the
aligned sequences in the same order than in |
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.
For clustalomega
, “clustalo” is the default on all systems
(with no specific path) since it seems there is no Windows installer.
The calculations 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 tempdir()
.
When called without arguments (i.e., clustal()
, ...), the
function prints the options of the program which may be passed to
MoreArgs
.
an object of class "DNAbin"
with the aligned sequences.
Emmanuel Paradis
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/Documentation/t_coffee/t_coffee_technical.htm
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.
image.DNAbin
, del.gaps
,
alex
, alview
, checkAlignment
The package ips which has similar functions for MAFFT and Prank.
## 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)