IQ-TREE

Introduction

IQ-TREE is an efficient phylogenomic software by maximum likelihood.

For more information, please check its website: https://biocontainers.pro/tools/iqtree and its home page: http://www.iqtree.org.

Versions

• 1.6.12

• 2.1.2

• 2.2.0_beta

• 2.2.2.2

Commands

• iqtree

Module

You can load the modules by:

module load biocontainers
module load iqtree

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run IQ-TREE on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=iqtree
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers iqtree

iqtree -s input.phy -m GTR+I+G > test.out