PRANK

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

PRANK is available as a module on Apocrita.

Usage

To run the default version of PRANK, simply load the prank module:

$ module load prank
$ prank -help

prank v.123456. Minimal usage: 'prank sequence_file'

Advanced usage:
  'prank [optional parameters] -d=sequence_file [optional parameters]'

For full usage documentation, run prank -help.

Core Usage

PRANK does not support multiple threads, so you must use #$ -pe smp 1 when using PRANK.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load prank

# align the FASTA sequences and output in HSAML format
prank -d=input_file \
      -t=tree_file \
      -o=output_file \
      -F -showxml

Reference

• PRANK website