Pplacer

Introduction

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment, guppy does all of the downstream analysis of placements, and rppr does useful things having to do with reference packages. For more information, please check: BioContainers: https://biocontainers.pro/tools/pplacer Home page: https://matsen.fhcrc.org/pplacer/

Versions

  • 1.1.alpha19

Commands

  • pplacer

  • guppy

  • rppr

Module

You can load the modules by:

module load biocontainers
module load pplacer

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 pplacer on our clusters:

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

module --force purge
ml biocontainers pplacer