cafe
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'cafe' Versions
- 4.2.1
- 5.0.0
Link to section 'Commands' of 'cafe' Commands
- cafe
Link to section 'Module' of 'cafe' Module
You can load the modules by:
module load biocontainers
module load cafe
Link to section 'Example job' of 'cafe' Example job
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