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.

RAxML-NG

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