Running IQ-Tree

Author:Brant C. Faircloth
Copyright:This documentation is available under a Creative Commons (CC-BY) license.

Modification History

See Running IQ-Tree


IQ-Tree is a program to infer ML trees from multiple sequence alignment and to perform analyses of those (and other) trees. We can analyze data in lots of different ways. Here, we’ll cover using IQ-Tree to analyze a concatenated data set and also to analyze a set of alignments to infer gene trees.

Preliminary Steps

  1. To compile Pargenes, see Compiling IQ-tree

Data Preparation

  1. IQ-Tree accepts data in a multitude of formats: PHYLIP, FASTA, NEXUS, CLUSTALW. Setup directory structure on @hpc to contain these data. Generally speaking, I make a project-specific folder within my work directory (where work is symlinked to /work/brant. So, using some fish data as an example:

    mkdir work/fish-analyses
    cd fish-analyses
    mkdir alignments
  2. On the transfer machine (@tabasco), navigate to the directory holding the alignment files and transfer the alignments files to @hpc (in this case, @supermic):

    rsync -avLP ./ [email protected]:/home/brant/work/fish-analyses/alignments


Unlike RAxML-NG, IQ-Tree does not require initial conversion of the data to a binary file.

Concatenated Alignments

This is pretty straightforward. One thing to keep in mind is that IQ-Tree parallelizes poorly when you are analyzing partitioned alignments - these I would usually run in raxml-ng.

Inferring the Best ML Tree (with ultra-fast bootstrapping)

  1. Sync up your concatenated alignment file. IQ-Tree does not require that you turn your alignment into a binary.

  2. Setup the following qsub file. Note that we’re simply appyling GTR+Gamma to the entire concatenated alignment here:

    #PBS -A <your allocation>
    #PBS -l walltime=24:00:00
    #PBS -l nodes=13:ppn=20
    #PBS -q checkpt
    #PBS -V
    #PBS -N iqtree-nopart
    #PBS -o iqtree-nopart-mpi.out
    #PBS -e iqtree-nopart-mpi.err
    module load gcc/6.4.0
    module load impi/2018.0.128/intel64
    export TASKS_PER_HOST=1  # number of MPI tasks per host
    export THREADS_HOST=20   # number of threads spawned by each task on the host
    mpirun -perhost ${NPERNODE:=1} -np ${PBS_NUM_NODES} -hostfile $PBS_NODEFILE \
        /project/brant/shared/bin/iqtree-omp-mpi \
        -s <your_alignment>.phy \
        -m GTR+G \
        -bb 1000 \
        -nt $THREADS_HOST

Individual Alignments

For individual alignments, the data that we uploaded consist of a directory of aligmments (zipped or unzipped, doesn’t really matter). We basically need to run IQ-Tree against each of the alignment files in the directory. As it does this, it will infer the best substitution model for each locus, then use that to infer the tree.

  1. Prep a list of alignment files that we will feed to IQ-Tree so that it know which trees we want to infer.

    # remove any existing list of loci to align
    rm trees-to-generate.list
    # loop over loci to build an input file
    for FULLPATH in $PWD/alignment-files-clean/*; do
        echo "$FULLPATH" >> trees-to-generate.list
  2. Prep the script that will actually run IQ-Tree named As written, this does not run any bootstrapping for a given locus. If you want to do that, add the -bb 1000 option to infer 1000 ultra-fast bootstraps. Note that we are setting the number of cores needed for each alignment to 2 here (you may need to increase as needed for larger alignments):

    ## set this manually
    ## DO NOT EDIT - this comes as input from GNU parallel on STDIN, via the sample.list file
    ## Here are the specific commands we are running
    # run iqtree
    /project/brant/shared/bin/iqtree -s $ALIGN -nt $CORES_PER_JOB
  3. Make sure to make this script executable: chmod 0755

  4. Create a qsub script to run the job and specify the number of nodes/cores you will need. Note that we are also declaring the number of CPUs per alignment here:

    #PBS -A <your allocation>
    #PBS -l nodes=1:ppn=20
    #PBS -l walltime=2:00:00
    #PBS -q checkpt
    #PBS -N multi_iqtree
    module load gnuparallel/20170122
    # Number of Cores per job (needs to be multiple of 2)
    export CORES_PER_JOB=2
    # move into the directory containing this script
    # set the number of Jobs per node based on $CORES_PER_JOB
    parallel --colsep '\,' \
            --progress \
            --joblog logfile.$PBS_JOBID \
            -j $JOBS_PER_NODE \
            --slf $PBS_NODEFILE \
            --workdir $PBS_O_WORKDIR \
            -a trees-to-generate.list \
            ./ {$1}
  5. Submit the job: qsub pasta.qsub. Be sure to monitor the job with checkjob -j <job_number> to ensure you are using resources approriately. You can also see how many trees have been inferred by running ls alignment-files-clean/*.treefile | wc -l.