Difference between revisions of "RAxML"

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* 1.0.5-Light
* 1.0.5-Light
* 7.3.0 (Standard)
* 7.3.0 (Standard)
* - 2012-02-20 upstream code update.
* - 2012-03-07 upstream code update (default).
==Variants of RAxML standard==
==Variants of RAxML standard==
* OpenMP threaded version - <code>/apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3</code>
* OpenMP threaded version - <code>/apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3</code>

Revision as of 19:39, 8 March 2012


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RAxML (Randomized Axelerated Maximum Likelihood) written by Alexandros Stamatakis and others is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package. Template:App Location

Installed Versions

  • 1.0.5-Light
  • 7.3.0 (Standard)
  • - 2012-02-20 upstream code update.
  • - 2012-03-07 upstream code update (default).

Variants of RAxML standard

  • OpenMP threaded version - /apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3
  • OpemMPI/OpenMP MPI and threaded hybrid version - /apps/RAxML/7.3.0/raxmlHPC-HYBRID-SSE3
  • OpenMPI version - /apps/RAxML/7.3.0/raxmlHPC-MPI

Running the application using modules

To use raxml with the environment modules system at HPC the following commands are available:

Get module information for raxml:

$module spider raxml

Load the application module:

$module load raxml

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_RAXML_DIR - directory where raxml is located.

To run the OpenMPI version load the following modules

module load intel/10.1 openmpi/1.2.7 raxml/7.3.0