Introduction
============

MView reformats the results of a sequence database search (BLAST, FASTA, etc)
or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup
to control colouring and web page layout. It can also be used as a filter to
extract and convert searches or alignments to common formats.


Requirements
^^^^^^^^^^^^

MView is implemented in Perl, version 5 as a self-contained command line
program that should run cross-platform.


Download
^^^^^^^^

The `latest version`_ of the software can be downloaded from the SourceForge
MView project as a UNIX/Linux bzipped or gzipped tar archive.

.. _latest version: https://sourceforge.net/projects/bio-mview


Installation
^^^^^^^^^^^^

1. Save the archive to your software area, e.g., ``/usr/local``, then uncompress
   and extract it using of these methods, depending on which archive format you
   downloaded.
 
   For the bzipped archive, one of::

     tar xvjf mview-1.59.tar.bz2

     bunzip2 < mview-1.59.tar.bz2 | tar xvf -

   For the gzipped archive, one of::

     tar xvzf mview-1.59.tar.gz

     gunzip < mview-1.59.tar.gz | tar xvf -

   This would create a directory called ``mview-1.59`` and place all the files
   under there.

2. Change to this directory and load ``bin/mview`` into an editor.

3. Set a Perl interpreter path valid for your machine after the '#!' magic
   number.

4. Change the ``use lib 'path/to/my/lib';`` line to, in our example::

     use lib '/usr/local/mview-1.59/lib';

5. Finally, add mview to somewhere on your PATH and rehash or login again.

Ask your system manager or a Perl guru for help if this looks weird.


Found a bug?
^^^^^^^^^^^^

Please send an email to *biomview _at_ gmail.com*. If MView isn't able to
parse your input file or produces a warning message, it would be very helpful
if you can include/attach the data file in your email so that I can
(1) quickly reproduce the error, and (2) add the example to the test suite.


Citation
^^^^^^^^

If you use MView in your work, please cite:

    Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database
    search or multiple alignment viewer. *Bioinformatics*. **14**\
    (4):380-381.  `PubMed
    <http://www.ncbi.nlm.nih.gov/pubmed/9632837?dopt=Abstract>`_


Copyright and licence
^^^^^^^^^^^^^^^^^^^^^

MView and associated libraries are Open Source Software with copyright
protected under the `GNU General Public License, version 2`_.

.. _GNU General Public License, version 2: etc/Licence.html


Acknowledgements
^^^^^^^^^^^^^^^^

People who contributed early code or suggestions include C. Leroy and other
members of the former Sander group at EBI. Useful suggestions relating to the
EBI sequence database search services have come from R. Lopez, W. Li
and H. McWilliam at EBI. Many other people have suggested new features and
reported bugs; I hope I have acknowledged them in the change log and apologise
if I have missed anyone out.

.. END
