RAxML

Please note that this application page is referring to the old CentOS software stack which is obsolete and does not work any more with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page.

Category

Bioinformatics

Description

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
	8.2.4

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
8.2.4	module load gcc/4.8.2 open_mpi/1.6.5 raxml/8.2.4

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a RAxML job in batch mode with the following command:

sbatch [Slurm options] --wrap="raxmlHPC-HYBRID-AVX [raxml options]"

or

sbatch [Slurm options] --wrap="raxmlHPC-PTHREADS-AVX [raxml options]

Here you need to replace [raxml options] with raxml command line options (please run raxmlHPC-HYBRID-AVX -h for getting a list of all command line options) and [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.

License information

GPLv3

Links

http://sco.h-its.org/exelixis/web/software/raxml

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf
https://github.com/stamatak/standard-RAxML