Software: VeryFastTree
Description
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.
Available Versions
| Unspecified: | 3.2.1 |
|---|
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
Commands
- VeryFastTree
Module
You can load the modules by:
module load biocontainers
module load veryfasttree
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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