proteinortho.rst

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