clustal

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Multiple Sequence Alignment with External Applications

These functions call their respective program from Rto align a set of nucleotide sequences of class "DNAbin".

Keywords
manip
Usage
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)
Arguments
x
an object of class "DNAbin".
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. clustal tries to guess it depending on the operating system (see details).
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 x.
Details

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 tempdir().

When called without arguments (i.e., clustal(), ...), the function prints the options of the program which may be passed to MoreArgs.

Value

  • an object of class "DNAbin" with the aligned sequences.

References

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

See Also

image.DNAbin, del.gaps, alex

The package phyloch which has similar functions for the MAFFT and Prank.

Aliases
  • clustal
  • muscle
  • tcoffee
Examples
### 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")
Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)

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