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IQ-TREE

IQ-TREE is fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood.[1]

Installed Versions♯

IQ-TREE 2.0.6 is installed. Use the modulefile:

iqtree/2.0.6

Example Job Script♯

The executable is iqtree2. The number of threads must be specified, and should be equal to the number CPU cores requested in the job.

The following job requests:

  • one (1) node
  • eight (8) CPU cores
  • 3 GB of memory per CPU core requested (i.e. 24 GB total)
  • maximum of 8 hours of run time
#!/bin/bash
#SBATCH --partition=def
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=3G
#SBTACH --time=8:00:00

module load iqtree/2.0.6

iqtree2 -nt $SLURM_CPUS_PER_TASK -s example.phy

References♯

[1] IQ-TREE website