Trimal

Introduction

Trimal is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.

For more information, please check its website: https://biocontainers.pro/tools/trimal and its home page: http://trimal.cgenomics.org.

Versions

• 1.4.1

Commands

• trimal

• readal

• statal

Module

You can load the modules by:

module load biocontainers
module load trimal

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 Trimal on our clusters:

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

module --force purge
ml biocontainers trimal

trimal -in input.fasta -out output1 -htmlout output1.html -gt 1