Muscle: MUSCLE alignment
In rPlant: Interface to the Agave API

Description Usage Arguments Details Value See Also Examples

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/

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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)

`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.

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.

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.

SubmitJob, Validate, UploadFile

## 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")