pplacer
Link to section 'Introduction' of '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/
Link to section 'Versions' of 'pplacer' Versions
- 1.1.alpha19
Link to section 'Commands' of 'pplacer' Commands
- pplacer
- guppy
- rppr
Link to section 'Module' of 'pplacer' Module
You can load the modules by:
module load biocontainers
module load pplacer
Link to section 'Example job' of 'pplacer' 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 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