Proteinortho

Introduction

Proteinortho is a tool to detect orthologous genes within different species.

For more information, please check its website: https://biocontainers.pro/tools/proteinortho and its home page on Gitlab.

Versions

  • 6.0.33

Commands

  • proteinortho

  • proteinortho2html.pl

  • proteinortho2tree.pl

  • proteinortho2xml.pl

  • proteinortho6.pl

  • proteinortho_cleanupblastgraph

  • proteinortho_clustering

  • proteinortho_compareProteinorthoGraphs.pl

  • proteinortho_do_mcl.pl

  • proteinortho_extract_from_graph.pl

  • proteinortho_ffadj_mcs.py

  • proteinortho_formatUsearch.pl

  • proteinortho_grab_proteins.pl

  • proteinortho_graphMinusRemovegraph

  • proteinortho_history.pl

  • proteinortho_singletons.pl

  • proteinortho_summary.pl

  • proteinortho_treeBuilderCore

Module

You can load the modules by:

module load biocontainers
module load proteinortho

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 Proteinortho on our clusters:

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

module --force purge
ml biocontainers proteinortho

proteinortho6.pl test/C.faa test/E.faa test/L.faa test/M.faa