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.
See which versions of fasttree are available:
$ module avail fasttree
Load one version into your environment and run it:
$ module load fasttree/2.1.11 $ FastTree
*Note:* if you're using the multi-threaded FastTreeMP please specify the number of CPU threads to use with the OMP_NUM_THREADS environment variable:
$ export OMP_NUM_THREADS=3 $ FastTreeMP
The number of CPU threads you choose should match the number of CPUs requested in your SLURM SBATCH allocation.
Notes from the sysadmin during installation:
$ sudo mkdir -p /export/apps/fasttree/2.1.11/bin $ sudo wget http://www.microbesonline.org/fasttree/FastTree -O /export/apps/fasttree/2.1.11/bin/FastTree $ sudo wget http://meta.microbesonline.org/fasttree/FastTreeMP -O /export/apps/fasttree/2.1.11/bin/FastTreeMP $ sudo chmod +x /export/apps/fasttree/2.1.11/bin/FastTree*