IQ-Tree

IQ-Tree is software used to infer phylogenetic trees by maximum likelihood.

Availability

Cluster	Module/Version
BOSE	iqtree/2.4.0 iqtree/3.1.3
BGSC	Not Available

Note: You can simply use module load iqtree to activate the most recently installed version of this software.

Running IQ-Tree 2 vs IQ-Tree 3

For convience, you can use the iqtree command for both modules. However, you can still use iqtree2 or iqtree3 depending on the version you are running.

Arguments / Options

This is a list of arguments for the iqtree command that we wanted to highlight.

Option	Description
--help	Full list of arguments available for the `iqtree` command
-T $SLURM_NTASKS	Set number of threads to Slurm cores, or set to "AUTO" when using `--threads-max`
--threads-max $SLURM_NTASKS	Set max number of threads to Slurm cores iqtree can use.
--mem NUM[G,M,%]	Specify the max amount of memory IQ-Tree uses. If used, make sure it's less than what you request using Slurm's `--mem` argument.

Sample Slurm Script

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 iqtree/3.1.3    # Load IQ-Tree
iqtree -T AUTO --threads-max $SLURM_NTASKS -s example.cf -m HKY+P

Real Example

Has your research group used IQ-Tree in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation(s) in your papers to support continued development of IQ-Tree.

Version 2:

B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. https://doi.org/10.1093/molbev/msaa015

Version 3:

Thomas KF Wong, Nhan Ly-Trong, Huaiyan Ren, Piyumal Demotte, Hector Banos, Andrew J Roger, Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W Hahn, Mario dos Reis, Le Sy Vinh, Gavin Huttley, Robert Lanfear, Bui Quang Minh (2026) IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Mol. Biol. Eviol.. https://doi.org/10.1093/molbev/msag117

Citing IQ-Tree

We highly recommend reviewing the official "How to cite IQ-Tree" page on IQ-Tree's website as it includes additional citations based on how you use the software.