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.
1 2 3 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.