POZITIV: Normalised Smith-Waterman alignments
---------------------------------------------
	
Authors:  Hilary Booth, Ole Nielsen, Shev McNamara
Email:    Hilary.Booth@anu.edu.au
Version:  1.0
Date:     11 February 2003
------------------------------------------------



OVERVIEW
--------


See the file DOC for more information on the components and their
interplay.


INSTALLATION AND TEST (UNIX)
----------------------------

1: Uncompress and unpack the tarball

2: Compile the C-extensions:
     python install.py
	   
3: Run tests
     python test_all.py
     
4: Run example:
     python ./doit.py	 (sequentially)

     
	

PARALLELISM
-----------

The alignment algorithms can make use of parallel architectures through the
use of message passing (MPI) adapted to Python in the form of
pypar [1].
Pre-requisites for parallel execution:

- Parallel platforms include Beowulf clusters, 
  Sun Enterprise multiprocessors and Compaq Alphaserver
  
- A native version of MPI (e.g. LAM-MPI or MPICH).	

- Pypar, the Python MPI interface

- Numerical Python  


To execute in parallel on four processors write     

  mpirun -np 4 ./demo.py 

or (on e.g. Alpha clusters)

  prun -n 4 ./demo.py

depending on the local MPI installation.



DISCLAIMER
----------
The POZITIV software consists of research codes that are constantly 
under development and we assume no responsibility whatsoever
for correctness or damage done as a consequence of using them.


LICENSE
-------
    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License (http://www.gnu.org/copyleft/gpl.html)
    for more details.

    You should have received a copy of the GNU General Public License
    along with this program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307


    Contact addresses: 
    	Hilary.Booth@anu.edu.au 
	Ole.Nielsen@anu.edu.au
	mcnamara@maths.anu.edu.au


   
ACKNOWLEDGEMENTS  
----------------
  This work was supported by 
  - Mathematical Sciences Institute (MSI), Australian National University.   
  - Centre for Bioinformation Science (CBiS), Australian National University.
  - Australian Partnership for Advanced Computing (APAC).



REFERENCES
----------

[1] pypar - a message passing interface for Python
    http://datamining.anu.edu.au/~ole/pypar/