CoreBio is a python toolkit for writing computational biology applications. For
further information on the CoreBio API, please consult the source code or the
API docmentation at 'docs/apidocs/index.html'.

o data:
    Standard information used in computational biology.
o db:
    Database access: astral, scop ...
o moremath:
    Various bits of useful math not in the standard python library.
o secstruc:
    Protein secondary structure and associated tools and data.
o seq:
    Alphabetic sequences and associated tools and data.
o seq_io:
    Sequence file reading and writing: array, clustal, fasta, genbank,
    intelligenetics, msf, nbrf, nexus, phylip, plain, stockholm, tabular.
o ssearch_io:
    Parse the output of BLAST and similar sequence search reports.
o transform:
    Transformations of Seqs (alphabetic sequences).
o utils:
    Extra utilities and core classes not in standard python.


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Installation
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CoreBio requires python version 2.3, 2.4 or 2.5. The following command will
quickly determine if python is available.
(Download python : http://www.python.org/download/)
    > python -V
    Python 2.4.2

If you have setuptools installed (http://peak.telecommunity.com/DevCenter/),
then installation can be accomplished with a single command:
    > sudo easy_install corebio

Or to upgrade:
    > sudo easy_install -U corebio

Alternativly, download the latest distribution from the project home
page, http://code.google.com/p/corebio/
    > curl http://corebio.googlecode.com/svn/dist/CoreBio-X.X.X.tar.gz >CoreBio.tar.gz
    > tar -zxf CoreBio.tar.gz
    > cd CoreBio-X.X.X

To install corebio from the main CoreBio directory:
    > python setup.py --help install # Show installation options
    > python setup.py install # Install code.
    > python setup.py install --home ~/local # Install into alternative location



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Development and Subversion Installation
---------------------------------------
To modify or extent CoreBio, or to use the latest code, obtain the source
directly from the subversion repository. (Subversion clients can be obtained at
 http://subversion.tigris.org)

> svn checkout http://corebio.googlecode.com/svn/trunk/ corebio

See the DEVELOPERS.txt file for more information.


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Distribution and Modification
-----------------------------

This package is distributed under the new BSD Open Source License.
Please see the LICENSE.txt file for details on copyright and licensing.