Paml

Introduction

Paml is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

For more information, please check its website: https://biocontainers.pro/tools/paml and its home page: http://abacus.gene.ucl.ac.uk/software/paml.html.

Versions

  • 4.9

Commands

  • baseml

  • basemlg

  • chi2

  • codeml

  • evolver

  • infinitesites

  • mcmctree

  • pamp

  • yn00

Module

You can load the modules by:

module load biocontainers
module load paml

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 Paml on our clusters:

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

module --force purge
ml biocontainers paml