Phast

Introduction

PHAST is a freely available software package for comparative and evolutionary genomics. For more information, please check: BioContainers: https://biocontainers.pro/tools/phast Home page: http://compgen.cshl.edu/phast/

Versions

  • 1.5

Commands

  • all_dists

  • base_evolve

  • chooseLines

  • clean_genes

  • consEntropy

  • convert_coords

  • display_rate_matrix

  • dless

  • dlessP

  • draw_tree

  • eval_predictions

  • exoniphy

  • hmm_train

  • hmm_tweak

  • hmm_view

  • indelFit

  • indelHistory

  • maf_parse

  • makeHKY

  • modFreqs

  • msa_diff

  • msa_split

  • msa_view

  • pbsDecode

  • pbsEncode

  • pbsScoreMatrix

  • pbsTrain

  • phast

  • phastBias

  • phastCons

  • phastMotif

  • phastOdds

  • phyloBoot

  • phyloFit

  • phyloP

  • prequel

  • refeature

  • stringiphy

  • treeGen

  • tree_doctor

Module

You can load the modules by:

module load biocontainers
module load phast

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 phast on our clusters:

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

module --force purge
ml biocontainers phast