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