_         _       _             
                 _ __   ___  __ _| | _____ | | __ _| |_ ___  _ __ 
                | '_ \ / _ \/ _` | |/ / _ \| |/ _` | __/ _ \| '__|
                | |_) |  __/ (_| |   < (_) | | (_| | || (_) | |   
                | .__/ \___|\__,_|_|\_\___/|_|\__,_|\__\___/|_|   
                |_|     



                Copyright (C) 2010 by Daniel Jones <dcjones@cs.washington.edu>
                All rights reserved.                           

                This software should not be redistributed or used for any commercial
                purpose without written permission from the author.

                This software is provided ``AS IS'' and any express or implied
                warranties, including, but not limited to, the implied warranties of
                merchantability and fitness for a particular purpose, are disclaimed.
                In no event shall the authors or the University of Washington be
                liable for any direct, indirect, incidental, special, exemplary, or
                consequential damages (including, but not limited to, procurement of
                substitute goods or services; loss of use, data, or profits; or
                business interruption) however caused and on any theory of liability,
                whether in contract, strict liability, or tort (including negligence
                or otherwise) arising in any way out of the use of this software, even
                if advised of the possibility of such damage.




Installation Intructions
------------------------

Make sure you have the prerequisites listed below installed. Then,

./configure && make install


Prerequisites
-------------

Python (>=2.6) http://www.python.org/
Cython         http://www.cython.org/
GSL            http://www.gnu.org/software/gsl/
NLopt          http://ab-initio.mit.edu/wiki/index.php/NLopt



Usage
-----

The script 'peakolate' is responsible for performing the scan.

Run, 'peakolate --help' for basic instructions.

the sequencing bias model can be trained with 'peakolate-seqbias'.