Cafe

Introduction

Cafe is a computational tool for the study of gene family evolution.

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

Versions

• 4.2.1

• 5.0.0

Commands

• cafe

Module

You can load the modules by:

module load biocontainers
module load cafe

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 Cafe on our clusters:

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

module --force purge
ml biocontainers cafe

#To get a list of commands just call CAFE with the -h or --help arguments
cafe5 -h

#To estimate lambda with no among family rate variation issue the command
cafe5 -i mammal_gene_families.txt -t mammal_tree.txt