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