fasttree
Link to section 'Introduction' of '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/
- 2.1.10
- 2.1.11
Link to section 'Commands' of 'fasttree' Commands
- fasttree
- FastTree
- FastTreeMP
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.
Link to section 'Module' of 'fasttree' Module
You can load the modules by:
module load biocontainers
module load fasttree
Link to section 'Example job using single CPU' of 'fasttree' Example job using single CPU
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
Link to section 'Example job using multiple CPUs' of 'fasttree' Example job using multiple CPUs
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