muscle {microseq} | R Documentation |
Computing a multiple sequence alignment using the MUSCLE software.
muscle(in.file, out.file, quiet = FALSE, diags = FALSE, maxiters = 16)
in.file |
Name of FASTA-file with input sequences. |
out.file |
Name of file to store the result. |
quiet |
Logical, |
diags |
Logical, |
maxiters |
Maximum number of iterations. |
The software MUSCLE (Edgar, 2004) must be installed and available on the system. Test this by typing
system("muscle")
in the Console, and some sensible output should be produced. NOTE: The executable must
be named muscle
on your system, no version numbers etc. For more details
on MUSCLE, see http://www.drive5.com/muscle.
By default diags=FALSE
but can be set to TRUE
to increase speed. This should be done only
if sequences are highly similar.
By default maxiters=16
. If you have a large number of sequences (a few thousand), or they are
very long, then this may be too slow for practical use. A good compromise between speed and accuracy is to run
just the first two iterations of the algorithm. On average, this gives accuracy equal to T-Coffee
and speeds much faster than CLUSTALW. This is done by the option maxiters=2
.
The result is written to the file specified in out.file
.
Lars Snipen.
Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792-1797.
## Not run: ex.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.fasta") muscle(in.file=ex.file,out.file="deleteMe.fasta") ## End(Not run)