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Software: PHAST

Description

PHAST is a freely available software package for comparative and evolutionary genomics.

Available Versions

Available Versions
Unspecified: 1.5

For more information, please check: BioContainers: https://biocontainers.pro/tools/phast
Home page: http://compgen.cshl.edu/phast/

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

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