PHYLIP_Pars: PHYLIP 3.69
In rPlant: R interface to the Agave and Foundation API

Description Usage Arguments Details Value See Also Examples

PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. The web page: http://evolution.genetics.washington.edu/phylip/doc/main.html, by Joe Felsenstein of the Department of Genome Sciences and the Department of Biology at the University of Washington, contain information on PHYLIP. PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees.

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PHYLIP_Pars(file.name, file.path="", job.name=NULL, type="DNA",
            print.curl=FALSE, shared.username=NULL, 
            suppress.Warnings=FALSE, email=TRUE)

`file.name`	Name of file to be evaluated on the Discovery Environment (DE).
`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
`type`	Two options "PROTEIN" or "DNA". This defines the type of sequences in the file, either proteins or nucleotides.
`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.
`email`	By default an email will be sent to the user when the job finishes.

The input file format that is supported is the interleaved phylip format http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format.

PHYLIP Parsimony outputs trees in Newick format http://en.wikipedia.org/wiki/Newick_format.

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(DNA.fasta)
## Not run: write.fasta(sequences = DNA.fasta, names = names(DNA.fasta), file.out = "DNA.fasta")
## Not run: Validate("username","password")
## Not run: UploadFile("DNA.fasta", filetype="FASTA-0")
## Not run: myJobMuD <- Muscle("DNA.fasta", aln.filetype="PHYLIP_PARS", job.name="musclePHYdna")
## Not run: minWait = 5 # seconds
## Not run: maxWait = 1800 # 30 min in seconds
## Not run: Wait(myJobMuD$id, minWait, maxWait)
## Not run: myJobPhyD <- PHYLIP_Pars("phylip_pars.aln", file.path=paste("analyses/",myJobMuD$name,
                                  sep=""), job.name="phylipDNA")
## End(Not run)
## Not run: Wait(myJobPhyD$id, minWait, maxWait)
## Not run: RetrieveJob(myJobPhyD$id, c("outtree.nwk"))

## Not run: require(ape)
## Not run: read.tree(paste(getwd(), myJobPhyD$name, "outtree.nwk", sep="/")) -> Tree
## Not run: plot(Tree)