fasttree
Link to section 'Description' of 'fasttree' Description
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.
Link to section 'Versions' of 'fasttree' Versions
- Anvil: 2.1.10
Link to section 'Module' of 'fasttree' Module
You can load the modules by:
module load fasttree
Link to section 'Example job using single CPU' of 'fasttree' Example job using single CPU
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 load fasttree
FastTree alignmentfile > treefile
Link to section 'Example job using multiple CPUs' of 'fasttree' Example job using multiple CPUs
To run FastTree on our our clusters using multiple CPUs:
#!/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 load fasttree
export OMP_NUM_THREADS=24
FastTreeMP alignmentfile > treefile