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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