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Wise2

Wise2 is a program for aligning proteins or protein HMMs to DNA. Its key program is genewise, a program for aligning proteins or protein HMMs to DNA.

Wise2 is available as a module on Apocrita.

Usage

To run the latest installed version of Wise2, simply load the wise2 module:

$ module load wise2
$ genewise -help

Usage:   genewise <protein-file> <dna-file> in fasta format

For full usage documentation, run genewise -help.

Example job

Serial Job

Here is an example job using 1 core and 1G memory:

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

module load wise2

genewise road.pep human.genomic

References