Multiple Sequence Alignment with External Applications
These functions call their respective program from Rto align a set of
nucleotide sequences of class
clustal(x, pw.gapopen = 10, pw.gapext = 0.1, gapopen = 10, gapext = 0.2, exec = NULL, 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)
- 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.
- a character string giving the name of the program, with
its path if necessary.
clustaltries to guess it depending on the operating system (see details).
- 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
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
``C:/Program Files/ClustalW2/clustalw2'' under Windows.
The calculations are done in a temporary directory which is deleted
when Ris 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.
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
Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Research,
Notredame, C., Higgins, D. and Heringa, J. (2000) T-Coffee: A novel
method for multiple sequence alignments. Journal of Molecular
Biology, 302, 205--217.
### 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")