RAxML: RAxML

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.

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.

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.

Examples

Run this code

## 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")

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