clustal: Multiple Sequence Alignment with External Applications

In ape: Analyses of Phylogenetics and Evolution

Multiple Sequence Alignment with External Applications

Description

These functions call their respective program from R to align a set of nucleotide sequences of class "DNAbin" or "AAbin". 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 system.

This version includes an experimental version of muscle5 which calls MUSCLE5 (see the link to the documentation in the References below); muscle still calls MUSCLE version 3. Note that the executable of MUSCLE5 is also named ‘muscle’ by the default compilation setting.

The functions efastats and letterconf require MUSCLE5.

Usage

clustal(x, y, guide.tree, pw.gapopen = 10, pw.gapext = 0.1,
        gapopen = 10, gapext = 0.2, exec = NULL, MoreArgs = "",
        quiet = TRUE, original.ordering = TRUE, file)
clustalomega(x, y, guide.tree, exec = NULL,MoreArgs = "",
              quiet = TRUE, original.ordering = TRUE, file)
muscle(x, y, guide.tree, exec, MoreArgs = "",
        quiet = TRUE, original.ordering = TRUE, file)
muscle5(x, exec = "muscle", MoreArgs = "", quiet = FALSE,
        file, super5 = FALSE, mc.cores = 1)
tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE,
        original.ordering = TRUE)

efastats(X, exec = "muscle", quiet = FALSE)
letterconf(X, exec = "muscle")

Arguments

x	an object of class "DNAbin" or "AAbin" (can be missing).
y	an object of class "DNAbin" or "AAbin" used for profile alignment (can be missing).
guide.tree	guide tree, an object of class "phylo" (can be missing).
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 this argument 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 (TRUE by default).
file	a file with its path if results should be stored (can be missing).
super5	a logical value. By default, the PPP algorithm is used.
mc.cores	the number of cores to be used by MUSCLE5.
X	a list with several alignments of the same sequences with all with the same row order.

Details

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, and “clustalw2.exe” under Windows. For clustalomega, “clustalo[.exe]” is the default on all systems (with no specific path).

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

Since ape 5.1, clustal, clustalomega, and muscle can align AA sequences as well as DNA sequences.

Value

an object of class "DNAbin" or "AAbin" with the aligned sequences.

efastats returns a data frame.

letterconf opens the default Web brower.

Author(s)

Emmanuel Paradis, Franz Krah

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. https://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. http://www.clustal.org/

https://drive5.com/muscle5/

See Also

image.DNAbin, del.gaps, all.equal.DNAbin, alex, alview, checkAlignment

Examples

## Not run: 
### display the options:
clustal()
clustalomega()
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)

ape documentation built on May 29, 2024, 10:50 a.m.