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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 #SBATCH --ntasks=1 when using PRANK.

Example job

Serial job

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

#!/bin/bash
#SBATCH --ntasks=1        # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G  # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0      # (or -t 1:0:0) Request 1 hour runtime

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