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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

RAxML-NG

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood optimization. It is a from-scratch, faster and more user-friendly successor to RAxML.

License

Free to use and open source under GNU AGPLv3.

Available

  • Roihu: 2.0.2, via the bio-apps module.

Usage

RAxML-NG is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the RAxML-NG module:

module load bio-apps/v202603
module load raxml-ng/2.0.2

A typical maximum-likelihood tree search with bootstrap support:

raxml-ng --all --msa alignment.fasta --model GTR+G --bs-trees 100 --threads 8

Example batch script

#!/bin/bash
#SBATCH --job-name=raxml-ng
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load raxml-ng/2.0.2

raxml-ng --all --msa alignment.fasta --model GTR+G --bs-trees 100 --threads $SLURM_CPUS_PER_TASK

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information