Software: Raxml (Randomized Axelerated Maximum Likelihood)
Description
Raxml (Randomized Axelerated Maximum Likelihood) is a program for the Maximum Likelihood-based inference of large phylogenetic trees.
Available Versions
| Unspecified: | 8.2.12 |
|---|
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/.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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