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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.

IQ-TREE

IQ-TREE is efficient software for phylogenomic inference by maximum likelihood. It includes model selection (ModelFinder), ultrafast bootstrap approximation and a wide range of substitution models.

License

Free to use and open source under GNU GPLv2.

Available

  • Roihu: 2.4.0, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load iq-tree/2.4.0

IQ-TREE (version 2) is run with the iqtree2 command. For example, a tree search with model selection and ultrafast bootstrap:

iqtree2 -s alignment.phy -m MFP -B 1000 -T AUTO

Example batch script

#!/bin/bash
#SBATCH --job-name=iqtree
#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 iq-tree/2.4.0

iqtree2 -s alignment.phy -m MFP -B 1000 -T $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