RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. The RAxML home page is at https://github.com/stamatak/standard-RAxML.
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 script for the Mahuika cluster
#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.
Each of our RAxML environment modules contains multiple RAxML executables:
The combinations of Slurm settings and RAxML types which make sense are:
raxmlHPC-SSE3with one task on only one CPU.
raxmlHPC-PTHREADS-SSE3with one task running on multiple CPUs.
raxmlHPC-MPI-SSE3with multiple tasks, each running on one CPU.
raxmlHPC-HYBRID-SSE3with 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
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.