BioPerl

Software Summary

Mesabi

Default Module:

1.6.901

Other Modules Available:

1.6.901, 1.7.1, 1.7.6, 5.12.2, 5.12.2_bioperl_1.006901, 5.16.1

Last Updated On:

Tuesday, August 29, 2023

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

1.6.901

Other Modules Available:

1.6.901, 1.7.1, 1.7.6, 5.12.2, 5.12.2_bioperl_1.006901, 5.16.1

Last Updated On:

Tuesday, August 29, 2023

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Tuesday, August 29, 2023

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Biostatistics

Genetics

Software Description

BioPerl is a toolkit of Perl modules useful for building bioinformatics programs in perl. The collection of modules in bioperl makes it easy to develop bioinformatics applications for sequences analysis, as well as for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), and running and parsing the results from hundreds of bioinformatics applications (bioperl-run).

Software Documentation

Software Documentation Tabs

General Linux

To run this software in a Linux environment run the command:

module load bioperl

Below is an example of how to use a sequence object in your Perl script:

#!/usr/bin/perl -w

use Bio::Seq

Note that the location of the Perl binary may change depending on which module is loaded. For more information on a BioPerl module, use the perldoc command, e.g.:

perldoc Bio::Seq

BioPerl also provides a number of Perl scripts for different tasks which may be found in the directory

/soft/bioperl/VER/bin

where VER is the version of BioPerl you are using. More information, including documentation and tutorials, may be found at the the BioPerl homepage.

Additional Information