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Bioperl

Description

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

  • Puhti: Perl 5.30.0 with Bioperl 1.007002

Usage

In Puhti, bioperl can be taken in use with command: 

module load biokit
After this you can launch a bioperl program with command: 
perl my_bioperl_code.pm
Alternatively you can change the perl definition in the first line of your code to 
#!/bin/env perl
and execute the perl program: 
./my_bioperl_code.pm

Support

servicedesk@csc.fi

Manual

Last update: October 10, 2022