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RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.

RAxML Homepage

Available Modules

module load RAxML/8.2.12-gimkl-2022a


RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. The RAxML home page is at

Licensing requirements

RAxML is licensed under the terms of the GNU General Public License ("the GPL"), version 2 or (at your option) any later version. A copy of version 3 of the GPL as included with the RAxML software is available here.

Example scripts

Example script for the Mahuika cluster

#!/bin/bash -e

#SBATCH --job-name      RAxML_job
#SBATCH --time          01:00:00
#SBATCH --ntasks        1
#SBATCH --cpus-per-task 4
#SBATCH --mem           2G

module load RAxML/8.2.12-gimkl-2020a

srun raxmlHPC-PTHREADS-AVX -T $SLURM_CPUS_PER_TASK -m GTRCAT -s aln.fasta -n tree.out


raxmlHPC-AVX -help and the RAxML manual.

Parallel Versions

Each of our RAxML environment modules contains multiple RAxML executables:

  • raxmlHPC-AVX
  • raxmlHPC-SSE3
  • raxmlHPC-MPI-AVX
  • raxmlHPC-MPI-SSE3
  • raxmlHPC-HYBRID-SSE3

The combinations of Slurm settings and RAxML types which make sense are:

  • raxmlHPC-AVX or raxmlHPC-SSE3 with one task on only one CPU.
  • raxmlHPC-PTHREADS-AVX or raxmlHPC-PTHREADS-SSE3 with one task running on multiple CPUs.
  • raxmlHPC-MPI-AVX or raxmlHPC-MPI-SSE3 with multiple tasks, each running on one CPU.
  • raxmlHPC-HYBRID-AVX or raxmlHPC-HYBRID-SSE3 with multiple tasks, each of which runs on multiple CPUs.

MPI and HYBRID are only useful for bootstrapped trees.

For the multi-threaded cases (PTHREADS and HYBRID) you should tell RAxML how many threads to use with the RAxML option -T $SLURM_CPUS_PER_TASK.

The "AVX" executables use the AVX SIMD instructions, while the "SSE3" executables use the older and slower Intel SIMD (Single Instruction Multiple Data) instructions, which can be anywhere from 10% to 30% slower. There should be no need to use an SSE3 executable, unless you find that an AVX executable doesn't work for any reason.