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.
The BioPerl distribution and BioPerl project have the same name. The BioPerl distribution includes only 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:
- figure out the modules you need, for example
Bio::DB::EUtilities(this is typically the modules that areusein your code) - install them with
cpanm, for examplecpanm Bio::DB::EUtilities
Alternatively, some Linux distributions have packaged BioPerl and have it available through their package manager.
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.
See the HACKING.md file for details on the project
structure, such as building from source and running the test suite.