Bmge

Introduction

Bmge is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.

For more information, please check its website: https://biocontainers.pro/tools/bmge and its home page: https://bioweb.pasteur.fr/packages/pack@BMGE@1.12.

Versions

  • 1.12

Commands

  • bmge

Module

You can load the modules by:

module load biocontainers
module load bmge

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 Bmge on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bmge
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bmge

bmge -i seq.fa -t AA -o out.phy