RAxML Next Generation (RAxML-NG)

Overview

RAxML Next Generation is an improved version of RAxML offering better speed, flexibility, and user experience. It can be used to find the best-known ML tree from a phylogenic tree.

Availability

Cluster	Module/Version
BOSE	raxml-ng/1.1.0
BGSC	raxml-ng/0.9.0

Note: You can simply use "module load raxml-ng" to activate the most recently installed version of this software.

Sample Slurm Script

The following example references prim.phy, which is available for download from the official tutorial on GitHub.

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load raxml-ng  # Load RAxML Next Generation
raxml-ng --msa prim.phy --model GTR+G --prefix T4 --threads ${SLURM_NTASKS} --seed 2 --tree pars{25},rand{25}

Real Example

Has your research group used RAxML Next Generation in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of RAxML Next Generation.

Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2019) RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35 (21), 4453-4455 doi:10.1093/bioinformatics/btz305