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/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.5

BELL

1.5

GAUTSCHI

1.5

NEGISHI

1.5

SCHOLAR

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 -p wholenode        # Partition 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
module biocontainers phast

# Your phast workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers phast

# Your phast workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers phast

# Your phast workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers phast

# Your phast workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers phast

# Your phast workflow...