PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

References:

• Veidenberg A, Medlar A, Löytynoja A. Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization. Mol Biol Evol. 2016 Apr;33(4):1126-30.

• PRANK Homepage
• Type man prank after loading the module

• Module Name: PRANK (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • PRANK_HOME
  • PRANK_EXAMPLES
• Example files in $PRANK_EXAMPLES

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load PRANK
[user@cn3144 ~]$ prank -d=input_file -t=tree_file -o=output_file -F -showxml

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. PRANK.sh). For example:

#!/bin/bash
module load PRANK
prank -d=input_file -t=tree_file -o=output_file -F -showxml

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] PRANK.sh

Create a swarmfile (e.g. PRANK.swarm). For example:

prank -d=input_file_1 -t=tree_file -o=output_file_1 -F -showxml
prank -d=input_file_2 -t=tree_file -o=output_file_2 -F -showxml
prank -d=input_file_3 -t=tree_file -o=output_file_3 -F -showxml
prank -d=input_file_4 -t=tree_file -o=output_file_4 -F -showxml

Submit this job using the swarm command.

swarm -f PRANK.swarm [-g #] [-t #] --module PRANK