veryfasttree
Link to section 'Introduction' of 'veryfasttree' Introduction
VeryFastTree is a highly-tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments. It is important to highlight that VeryFastTree keeps unchanged the phases, methods and heuristics used by FastTree-2 to estimate the phylogenetic tree. In this way, it produces trees with the same topological accuracy than FastTree-2. In addition, unlike the parallel version of FastTree-2, VeryFastTree is deterministic.
BioContainers: https://biocontainers.pro/tools/veryfasttree
Home page: https://github.com/citiususc/veryfasttree
Link to section 'Versions' of 'veryfasttree' Versions
- 3.2.1
Link to section 'Commands' of 'veryfasttree' Commands
- VeryFastTree
Link to section 'Module' of 'veryfasttree' Module
You can load the modules by:
module load biocontainers
module load veryfasttree
Link to section 'Example job' of 'veryfasttree' Example job
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 veryfasttree on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=veryfasttree
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers veryfasttree