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.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/veryfasttree

Home page: https://github.com/citiususc/veryfasttree

Versions

• 3.2.1

Commands

• VeryFastTree

Module

You can load the modules by:

module load biocontainers
module load veryfasttree

Example job

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 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