FastTree
Introduction
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.
Detailed usage can be found here: http://www.microbesonline.org/fasttree/
Versions
2.1.10
2.1.11
Commands
fasttree
FastTree
FastTreeMP
Note
fasttree
and FastTree
are the same program, and they only support one CPU. If you want to use multiple CPUs, please use FastTreeMP
and also set the OMP_NUM_THREADS
to the number of cores you requested.
Module
You can load the modules by:
module load biocontainers
module load fasttree
Example job using single CPU
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run FastTree on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=fasttree
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers fasttree
FastTree alignmentfile > treefile
Example job using multiple CPUs
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run FastTree on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=FastTreeMP
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers fasttree
export OMP_NUM_THREADS=24
FastTreeMP alignmentfile > treefile