Multiple alignment using MUSCLE
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:
fa.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.faa")
muscle(in.file = fa.file, out.file = "delete_me.msa")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.