Bali-phy

Introduction

Bali-phy is a tool for bayesian co-estimation of phylogenies and multiple alignments via MCMC.

For more information, please check:

Versions

  • 3.6.0

Commands

  • bali-phy

Module

You can load the modules by:

module load biocontainers
module load bali-phy

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 bali-phy on our clusters:

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

module --force purge
ml biocontainers bali-phy

bali-phy examples/sequences/ITS/ITS1.fasta 5.8S.fasta ITS2.fasta --test
bali-phy examples/sequences/5S-rRNA/5d-clustalw.fasta -S gtr+Rates.gamma[4]+inv -n 5d-free