Raxml

Introduction

Raxml (Randomized Axelerated Maximum Likelihood) is a program for the Maximum Likelihood-based inference of large phylogenetic trees.

For more information, please check its website: https://biocontainers.pro/tools/raxml and its home page: https://cme.h-its.org/exelixis/web/software/raxml/.

Versions

  • 8.2.12

Commands

  • raxmlHPC

  • raxmlHPC-AVX2

  • raxmlHPC-PTHREADS

  • raxmlHPC-PTHREADS-AVX2

  • raxmlHPC-PTHREADS-SSE3

  • raxmlHPC-SSE3

Module

You can load the modules by:

module load biocontainers
module load raxml

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Raxml on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 36
#SBATCH --job-name=raxml
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers raxml

raxmlHPC-SSE3 -m GTRGAMMA  -p 12345 -s input.fasta -n HPC-SSE3_out -# 20 -T 36
raxmlHPC -m GTRGAMMA  -p 12345 -s input.fasta -n HPC_out -# 20 -T 36
raxmlHPC-AVX2  -m GTRGAMMA  -p 12345 -s input.fasta -n HPC-AVX2_out -# 20 -T 36
raxmlHPC-PTHREADS  -m GTRGAMMA  -p 12345 -s input.fasta -n HPC-PTHREADS_out -# 20 -T 36
raxmlHPC-PTHREADS-AVX2  -m GTRGAMMA  -p 12345 -s input.fasta -n HPC-PTHREADS-AVX2_out -# 20 -T 36
raxmlHPC-PTHREADS-SSE3  -m GTRGAMMA  -p 12345 -s input.fasta -n HPC-PTHREADS-SSE3_out -# 20 -T 36