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PRANK

Description

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

How to Use

PRANK uses environment modules. Type

module load PRANK

at the prompt.

To see the help menu, type

prank -help

at the prompt.

For online documentation, type

man prank

at the prompt.

Examples are available in $PRANKINSTALLDIR/examples:

cp $PRANKINSTALLDIR/examples/* .
bash script.sh

Usage on Helix and interactive nodes

prank -d=input_file -t=tree_file -o=output_file -F -showxml

Usage on Biowulf in batch

Create a batch script:

#!/bin/bash
# --- This file is example.sh --
  
module load PRANK
prank -d=input_file -t=tree_file -o=output_file -F -showxml

Submit with the appropriate sbatch command:

sbatch example.qsub

Usage on Biowulf as a swarm

Create a swarmfile:

# --- This file is example.swarm ---
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 with the appropriate swarm command:

swarm -f example.swarm --module PRANK

Documentation