muscle {microseq}

Multiple alignment using MUSCLE

Description

Computing a multiple sequence alignment using the MUSCLE software.

Usage

muscle(
  in.file,
  out.file,
  muscle.exe = "muscle",
  quiet = FALSE,
  diags = FALSE,
  maxiters = 16
)

Arguments

in.file

Name of FASTA file with input sequences.

out.file

Name of file to store the result.

muscle.exe

Command to run the external software muscle on the system (text).

quiet

Logical, quiet = FALSE produces screen output during computations.

diags

Logical, diags = TRUE gives faster but less reliable alignment.

maxiters

Maximum number of iterations.

Details

The software MUSCLE (Edgar, 2004) must be installed and available on the system. The text in muscle.exe must contain the exact command to invoke muscle on the system.

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.

Value

The result is written to the file specified in out.file.

Author(s)

Lars Snipen.

References

Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792-1797.

See Also

msaTrim.

Examples

## 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)