phast
Link to section 'Introduction' of '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/
Link to section 'Versions' of 'phast' Versions
- 1.5
Link to section 'Commands' of '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
Link to section 'Module' of 'phast' Module
You can load the modules by:
module load biocontainers
module load phast
Link to section 'Example job' of '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