Bio-Community
==========================


ABOUT

The Bio-Community distribution contains a set of generic, open, object-oriented,
cross-platform Perl modules to represent and manipulate communities of
biological organisms. Bio-Community is part of the BioPerl project
(http://bioperl.org/).


INSTALLATION & DEPENDENCIES

The Bio-Community modules require Perl 5.10 or above. Additionally, these Perl
modules are required and will be installed during the installation procedure:

 BioPerl version >= 1.6.923
 DateTime
 Getopt::Euclid
 JSON::XS
 Hash::Util
 Math::Random::MT
 Method::Signatures
 Module::Runtime
 Moose
 Moose::Util::TypeConstraints
 MooseX::NonMoose
 MooseX::StrictConstructor
 Parallel::Iterator
 PerlIO:eol
 Scalar::Util
 Tie::IxHash
 Test::Number::Delta

This other module is recommended:
 Math::BigInt::GMP

To install the Bio::Community modules, type the following:
  perl Build.PL
  ./Build installdeps   (as administrator)
  ./Build
  ./Build test
  ./Build install       (as administrator)


OVERVIEW

The ./lib/ folder contains the Bio-Community modules, which provide various
objects and operations:

* The main objects are the community, member and metacommunity, provided by
  Bio::Community, Bio::Community::Member and Bio::Community::Meta, respectively

* Reading and writing files in various formats, e.g. QIIME, biom, is possible
  through Bio::Community::IO

* Alpha, beta and gamma diversity metrics are implemented in the modules
  Bio::Community::Alpha, Bio::Community::Meta::Beta and Bio::Community::Meta::Gamma

* Bio::Community::Tools::* are modules providing various operations like random
  sampling, rarefaction or taxonomic summaries.

The ./scripts/ folder contains scripts. All these scripts use the Bio::Community
modules and are useful for reading or writing files, rarefying,
They are good examples of how Bio::Community modules can be used as building
blocks for more complex programs. For convenience, all scripts are prefixed with
'bc_'.

The ./t/ folder contains unit tests to ensure the proper functioning of the
Bio-Community mocules. The ./t/data/ further contains data files used for the
tests and is thus a good source of example data.


SUPPORT AND BUGS

User feedback is an integral part of the evolution of this and other Bioperl
modules. Please direct usage questions or support issues to the mailing list,
[email protected], 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.

If you have found a bug, please report it on the BioPerl bug tracking system
to help us keep track the bugs and their resolution:
https://redmine.open-bio.org/projects/bioperl/


COPYRIGHT

Copyright 2011,2012,2013 by the BioPerl Team <[email protected]>

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.

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