FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

References:

• FastTree is open-source software developed by Price et al. [FastTree paper]

• FastTree documentation

• Module Name: FastTree (see the modules page for more information)
• Singlethreaded (FastTree) and Multithreaded (FastTreeMP) versions are available.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load FastTree

[user@cn3144 ~]$ FastTreeMP  alignmentfile  > treefile
[....]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. FastTree.sh). For example:

#!/bin/bash
set -e

module load FastTree

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

FastTreeMP alignmentfile > treefile

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=4g FastTree.sh

If you need more than the default 4 GB of memory, add --mem=8g to the sbatch command line.

Create a swarmfile (e.g. FastTree.swarm). For example:

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK; FastTreeMP  alignment1 > tree1
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK; FastTreeMP  alignment2 > tree2
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK; FastTreeMP  alignment3 > tree3
[....]

Submit this job using the swarm command.

swarm -f FastTree.swarm [-g #] [-t #] --module FastTree