OrthoFinder

Introduction

OrthoFinder: phylogenetic orthology inference for comparative genomics

Detailed usage can be found here: https://github.com/davidemms/OrthoFinder

Versions

• 2.5.2

• 2.5.4

• 2.5.5

Commands

• orthofinder

Module

You can load the modules by:

module load biocontainers
module load orthofinder/2.5.4

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 orthofinder on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=orthofinder
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers orthofinder/2.5.4

orthofinder -t 24 -f InputData -o output