RAxML: RAxML

In rPlant: Interface to the Agave API

Description

RAxML (Randomized Accelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic tress. It originally had been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package. See http://bioinformatics.oxfordjournals.org/content/suppl/2014/01/18/btu033.DC1/NewManual.pdf for details. The app details can be found here: https://pods.iplantcollaborative.org/wiki/display/DEapps/RAxML-8.2.3_small_and_medium.

Usage

RAxML(file.name, file.path="", type="DNA", out.name=NULL, 
      model=NULL, bootstrap=NULL, algorithm="d", rseed=NULL,
      args=NULL, numcat=25, nprocs=12, job.name=NULL, 
      print.curl=FALSE, shared.username=NULL, small=TRUE,
      substitution.matrix=NULL, empirical.frequencies=FALSE,
      suppress.Warnings=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
out.name	the name to give the output files
type	Two options "PROTEIN" or "DNA". This defines the type of sequences in the file, either proteins or nucleotides.
rseed	(-p) required seed number, to replicate set this integer, otherwise it will randomly chosen
model	(-m) Substitution model. For DNA the choices are GTRCAT, GTRGAMMA, GTRCATI and GTRGAMMAI. For protein the choices are PROTCAT, PROTGAMMA, PROTCATI and PROTGAMMAI. The details p. 10-11 of manual.
substitution.matrix	This is only necessary for the protein alignments. The choices are: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU and GTR, the default is BLOSUM62
empirical.frequencies	(F) Only used for protein alighnments, with appendix you can specify if you want to use empirical base frequencies.
bootstrap	(-b) Random Seed Number for non-parametric bootstrapping, details bottom of p. 7 of manual
algorithm	(-f) Select the type of algorithm/function you want. "d" is default, details bottom of p. 8 of manual
numcat	(-c) Specify the number of distinct rate categories, details top of p. 13 of manual
nprocs	The number of processors to be allocated to the job, default = 12
small	The size of data set is small, if large set to small=FALSE
job.name	the name to give the job being submitted
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. Then the dir.path becomes the path to the SHARED user's shared folder.
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 RAxML model has much additional functionality that is not fit into this wrapper function (http://bioinformatics.oxfordjournals.org/content/suppl/2014/01/18/btu033.DC1/NewManual.pdf), see details. This option allows users to add anything that is not included (.i.e. args="-d"), which starts the RAxML search with a random starting tree, see detals.

Details

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

Additional arguments, args, can be found at http://bioinformatics.oxfordjournals.org/content/suppl/2014/01/18/btu033.DC1/NewManual.pdf. The args input is text with the flags and inputs for those flags in a string like on the command line.

For this application there are numerous output files. See pg 16-17 of the manual for complete details. RAxML outputs trees in Newick format http://en.wikipedia.org/wiki/Newick_format.

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

## Not run: data(phylip_interleaved_dna.aln)
## Not run: write.table(phylip_interleaved_dna.aln, "phylip_interleaved_dna.aln", 
                     quote=FALSE, row.names=FALSE, col.names=FALSE)
## End(Not run)
## Not run: Validate("username","password")
## Not run: UploadFile("phylip_interleaved_dna.aln")
## Not run: myJobRaxD <- RAxML("phylip_interleaved_dna.aln", job.name="raxmlDNAphy")

rPlant documentation built on April 14, 2017, 6:03 p.m.