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About BioPerl

BioPerl is a project for development of free and open source Perl tools for computational molecular biology. For example, it includes classes for biological sequences, readers of multiple formats, sequence alignments, database searching objects, and interfaces to multiple programs such as EMBOSS, ClustalW, and BLAST.

The BioPerl project has developed multiple module distributions for different purposes. The one named BioPerl (named after the project) provides the foundation for all others distributions.

This is the repository for the BioPerl distribution only. Other distributions have their own repositories.

Installation

BioPerl distribution has the same name as the BioPerl. However, the BioPerl distribution only includes a subset of the project modules. Because of this, the meaning of "installing BioPerl" is rarely clear. Instead of "install BioPerl", the aim must be "install module X".

CPAN.org provides an overview on how to install and manage Perl modules but the bottom-line is:

1. find the module you need, for example Bio::DB::EUtilities
2. install it with cpanm, for example cpanm Bio::DB::EUtilities

Alternatively, some Linux distributions have packaged BioPerl and have it available through their package manager.

Documentation and Support

Documentation for individual modules is in POD and can also be read online at metacpan. Useful documentation in the form of example code can also be found in the examples/ and bin/ directories.

Additional resources and information about the project is available on the project website, with discussion happening on the bioperl-l@bioperl.org mailing list, and on the #bioperl channel of the freenode IRC server.

Bug reports are handle on the distribution github page.

Development

See the HACKING.md file for details on the project structure, such as building from source and running the test suite.