FastTree
Overview
FastTree is a program to infer 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.
Versions 2.1.3 and 2.1.11 are installed on the CSF.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the GNU GPL v2 license and all usage must adhere to that license.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/intel-18.0/fasttree/2.1.11 # Serial and multi-core versions module load apps/fasttree/2.1.3 # Serial only
Running the application
Please do not run FastTree on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript # Choose the version you require module load apps/intel-18.0/fastree/2.1.11 # Serial version of the app (will use 1 CPU-core) # To infer a tree for a protein alignment with the JTT+CAT model, use FastTree alignment.file > tree_file # To infer a tree for a nucleotide alignment with the GTR+CAT model, use FastTree -gtr -nt alignment_file > tree_file
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
FastTree can use multiple CPU cores in a single-compute node. The executable program is called FastTreeMP. Note that the FastTree website contains the following information about the multi-core version:
- As of version 2.1,
FastTreeMPwill not give exactly the same results asFastTreebecause the top-hits heuristics become non-deterministic (depending on which seed is reached first) and because the star topology test is turned off. However, in practice, the results are of the same quality.
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory #$ -pe smp.pe 4 # Number of cores, can be 2--32 # NO -V line - we load modulefiles in the jobscript # Choose the version you require module load apps/intel-18.0/fastree/2.1.11 # Inform FastTreeMP how many cores to use. $NSLOTS is set to the number of cores above. export OMP_NUM_THREADS=$NSLOTS # To infer a tree for a protein alignment with the JTT+CAT model, use FastTreeMP alignment.file > tree_file # To infer a tree for a nucleotide alignment with the GTR+CAT model, use FastTreeMP -gtr -nt alignment_file > tree_file
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.