NAME

       BioPerl - Perl modules for biology

VERSION

       version 1.7.8

SYNOPSIS

       If you're new to BioPerl, you should start reading the BioPerl HOWTO's:

       <http://bioperl.org/howtos/index.html>

   References for Individual Modules
       For ease of maintenance and coordination amongst contributors, BioPerl code is maintained
       in a modular form, as is the documentation.  Refer to the documentation for individual
       modules by using perldoc, i.e.

       "perldoc Bio::Seq"

       to get documentation for the Bio::Seq object.

DESCRIPTION

       BioPerl is the product of a community effort to produce Perl code which is useful in
       biology. Examples include Sequence objects, Alignment objects and database searching
       objects. These objects not only do what they are advertised to do in the documentation,
       but they also interact - Alignment objects are made from the Sequence objects, Sequence
       objects have access to Annotation and SeqFeature objects and databases, Blast objects can
       be converted to Alignment objects, and so on. This means that the objects provide a
       coordinated and extensible framework to do computational biology.

       BioPerl development focuses on Perl classes, or code that is used to create objects
       representing biological entities. There are scripts provided in the scripts/ and examples/
       directories but scripts are not the main focus of the BioPerl developers. Of course, as
       the objects do most of the hard work for you, all you have to do is combine a number of
       objects together sensibly to make useful scripts.

       The intent of the BioPerl development effort is to make reusable tools that aid people in
       creating their own sites or job-specific applications.

       The BioPerl website at <http://bioperl.org> also attempts to maintain links and archives
       of standalone bio-related Perl tools that are not affiliated or related to the core
       BioPerl effort. Check the site for useful code ideas and contribute your own if possible.

INSTALLATION

       The BioPerl modules are distributed as a tar file that expands into a standard perl CPAN
       distribution. Detailed installation directions can be found in the distribution INSTALL
       file. Installing on windows using ActiveState Perl is covered in the INSTALL.WIN file.  We
       highly suggest reading the installation instructions on the BioPerl website:

       <http://bioperl.org/INSTALL.html>

       Note that only the following are supported at this time with the current API:

       BioPerl-db
       BioPerl-network
       BioPerl-run
       BioPerl-pedigree
       Bio::Graphics

GETTING STARTED

       The distribution scripts/ directory has working scripts for use with BioPerl, check the
       self-described examples/ directory as well. You are more than welcome to contribute your
       script!

       If you have installed BioPerl in the standard way, as detailed in the INSTALL in the
       distribution, these scripts should work by just running them.

GETTING INVOLVED

       BioPerl is a completely open community of developers. We are not funded and we don't have
       a mission statement. We encourage collaborative code, in particular in Perl. You can help
       us in many different ways, from just a simple statement about how you have used BioPerl to
       doing something interesting to contributing a whole new object hierarchy. See
       <http://bioperl.org> for more information. Here are some ways of helping us:

   Asking questions and telling us you used it
       We are very interested to hear how you experienced using BioPerl. Did it install cleanly?
       Did you understand the documentation? Could you get the objects to do what you wanted them
       to do? If BioPerl was useless we want to know why, and if it was great - that too. Post a
       message to bioperl-l@bioperl.org, the BioPerl mailing list, where all the developers are.

       Only by getting people's feedback do we know whether we are providing anything useful.

   Writing a script that uses it
       By writing a good script that uses BioPerl you both show that BioPerl is useful and
       probably save someone elsewhere writing it. If you contribute it to the 'script central'
       at <http://bioperl.org> then other people can view and use it.  Don't be nervous if you've
       never done this sort of work, advice is freely given and all are welcome!

   Find bugs!
       We know that there are bugs in this code. If you find something which you are pretty sure
       is a problem, post a bug report using our Bugzilla tracking system:

       <https://github.com/bioperl/bioperl-live/issues>

       Please read the main bug tracking (<http://www.bioperl.org/articles/Bugs.html>) for an
       overview of what we expect in a bug report. Specifically, having a code and data example
       where appropriate helps tremendously.  We gladly accept all patches after a quick code
       review.

   Suggest new functionality
       You can suggest areas where the objects are not ideally written and could be done better.
       The best way is to find the main developer of the module (each module was written
       principally by one person, except for Seq.pm). Talk to him or her and suggest changes.

   Make your own objects
       If you can make a useful object we will happily include it into the core.  Probably you
       will want to read a lot of the documentation in Bio::Root::Root and talk to people on the
       BioPerl mailing list, bioperl-l@bioperl.org.

   Writing documentation
       We appreciate good documentation. It's what tells the world what's in BioPerl, it's what
       instructs the user, it's what describes the rationale and inner workings of the package.
       Feel free to contribute.

ACKNOWLEDGEMENTS

       For a more detailed history of the BioPerl project, we recommend the History of BioPerl:

       <http://bioperl.org/articles/History_of_BioPerl.html>

FEEDBACK

   Mailing lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org               - General discussion
         https://bioperl.org/Support.html    - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org
       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR

       See the individual modules for their authors.

COPYRIGHT

       This software is copyright (c) by many people (see the individual modules for their
       copyright holders).

       This software is available under the same terms as the perl 5 programming language system
       itself.