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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 -O /export/apps/fasttree/2.1.11/bin/FastTree
$ sudo wget -O /export/apps/fasttree/2.1.11/bin/FastTreeMP
$ sudo chmod +x /export/apps/fasttree/2.1.11/bin/FastTree*
fasttree-software.txt · Last modified: 2020/08/09 12:52 by aorth