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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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: 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

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