"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)
"DNAbin"
.clustal
tries to guess it depending on
the operating system (see details).x
."DNAbin"
with the aligned sequences.
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
.
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)
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