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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-CPU: IQ-TREE 2 as iq-tree/2.4.0 and IQ-TREE 3 as iqtree3/3.1.4, via the bio-apps module. The two are separate modules with distinct commands (iqtree2 and iqtree3) and can be used side by side.

Usage

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

IQ-TREE 2 is run with the iqtree2 command:

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

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

IQ-TREE 3 is provided as a separate module and run with the iqtree3 command; the options are the same:

module load bio-apps/v202603
module load iqtree3/3.1.4

iqtree3 -s alignment.phy -m MFP -B 1000 -T AUTO

The examples above perform a tree search with model selection (ModelFinder) and ultrafast bootstrap.

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