MUSCLE alignment

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Description

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. The manual is also available here: http://www.drive5.com/muscle/manual/

Usage

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Muscle(file.name, file.path="", job.name=NULL, args=NULL,
       aln.filetype="PHYLIP_INT", shared.username=NULL, out.name=NULL,
       suppress.Warnings=FALSE, print.curl=FALSE)

Arguments

file.name

name of file to be evaluated on the Discovery Environment (DE), see details for supported input formats.

file.path

optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory

job.name

the name to give the job being submitted

out.name

name of the output file

aln.filetype

Muscle does alignment of sequences, this option selects the file type of that result file. There are six options PHYLIP_INT, PHYLIP_SEQ, HTML, FASTA, CLUSTALW, MSF, see details

print.curl

Prints the curl statement that can be used in the terminal, if curl is installed on your computer

shared.username

With iPlant you have the ability to share folders with other users. If someone has shared a folder with you and you want to run a job with them, enter their username for this input.

suppress.Warnings

This will turn off the warnings, will speed up run time. Use with caution, if the inputs are incorrect they will not be caught.

args

Optional for arguments (i.e. flags). The Muscle model has much additional functionality that is not fit into this wrapper function (http://www.drive5.com/muscle/muscle_userguide3.8.html#_Toc260497051), see details. This option allows users to add anything that is not included (.i.e. args="-spscore"), which computes SP objective score, see details.

Details

The supported input file format is the fasta format http://en.wikipedia.org/wiki/FASTA_format.

Additional arguments, args, can be found at http://www.drive5.com/muscle/muscle_userguide3.8.html#_Toc260497051. The args input is text with the flags and inputs for those flags in a string like on the command line.

There are six possible alignment output files, named appropriately: phylip_interleaved.aln http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format, phylip_sequential.aln http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format, html.aln http://sonnhammer.sbc.su.se/Belvu.html,fasta.aln http://en.wikipedia.org/wiki/FASTA_format, clustalw.aln http://meme.nbcr.net/meme/doc/clustalw-format.html, msf.aln http://en.wikipedia.org/wiki/MSF.

Value

A list containing the job id and the job name is provided for jobs submitted. If an error, then a message stating the error should also be reported.

See Also

SubmitJob, Validate, UploadFile

Examples

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## Not run: data(PROTEIN.fasta)
## Not run: write.fasta(sequences = PROTEIN.fasta, names = names(PROTEIN.fasta),
                     file.out = "PROTEIN.fasta")
## End(Not run)
## Not run: Validate("username","password")
## Not run: UploadFile("PROTEIN.fasta", filetype="FASTA-0")
## Not run: Muscle("PROTEIN.fasta", aln.filetype="FASTA", job.name="muscleAAfasta")