BioPerl

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do. On the other hand, BioPerl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs. Consequently, BioPerl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.

• BioPerl
  • License
  • Available
  • Usage
  • Support
  • More information

License

BioPerl is free to use and open source.

BioPerl is licensed under the same terms as Perl itself which is dually-licensed under the terms of the Perl Artistic license or GNU GPLv3.

Available

• Roihu-CPU: BioPerl 1.7.8 (module perl-bioperl), via the bio-apps module.

Usage

BioPerl is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BioPerl module:

module load bio-apps/v202603
module load perl-bioperl/1.7.8

After this, you can launch a BioPerl program with the command:

perl my_bioperl_code.pl

Alternatively you can set the interpreter on the first line of your script to

#!/usr/bin/env perl

make it executable, and run it directly:

chmod +x my_bioperl_code.pl
./my_bioperl_code.pl

Support

CSC Service Desk

More information

• BioPerl home page

Do you find this page useful?

Yes

Thank you for your feedback!

No

Thank you! Your feedback is appreciated.

Please let us know how we could improve this page by contacting us or by creating an issue in GitHub. You can also edit this page yourself and contribute your improvements by creating a pull request.