Bio::Tools::PSort::ModHMM version 0.01
======================================

TABLE OF CONTENTS
-----------------

1) DESCRIPTION
2) INSTALLATION
3) DEPENDENCIES
4) BUGS
5) Algorithm::HMM COPYRIGHT AND LICENCE
6) AUTHOR INFORMATION


1) DESCRIPTION
--------------

Bio::Tools::PSort::ModHMM was originally written by Matthew Laird of Simon
Fraser University Brinkman Laboratory and provides Perl bindings for
the Prodiv_TMHMM package by Hakan Viklund.

Bio::Tools::PSort::ModHMM is based on Prodiv_TMHMM, for more information
on Prodiv_TMHMM, see the package homepage at:

http://www.pdc.kth.se/~hakanv/prodiv-tmhmm/


The author invites feedback on Bio::Tools::PSort::ModHMM. If you find a
bug, please send the information described in the BUGS section below.


2) INSTALLATION
---------------

Bio::Tools::PSort::ModHMM has been tested under linux/x86, linux/i64,
other operating systems are not supported at this time.  However if you
require Bio::Tools::PSort::ModHMM under a different OS, please email us and we
can work with you to port it, lack of support is simply due to us
not having access to machines of other architectures.

For i64 installation instructions please see README.x86_64

Before installation, you will need to compile the libmodhmm library.
All the required source files for these libraries are contained
in the modhmm0.92b/ directory.  The library can be compiled as follows:

  cd modhmm0.92b/
  make
  cp libmodhmm.so /usr/local/lib

  ldconfig

Installation of the Bio::Tools::PSort::ModHMM module is then as follows:

   perl Makefile.PL
   make
   make test
   make install


3) DEPENDENCIES
---------------

Bio::Tools::PSort::ModHMM does require the libmodhmm library to be
compiled and installed.  This library is distributed with this
module.


4) BUGS
-------

If you find a bug, please report it to the author along with the
following information:

    * version of Perl (output of 'perl -V' is best)
    * version of Bio::Tools::PSort::ModHMM
    * operating system type and version
    * exact text of error message or description of problem
    * example model files/data being classified

If we don't have access to a system similar to yours, you may be asked
to insert some debugging lines and report back on the results.
The more help and information you can provide, the better.


5) Bio::Tools::PSort::ModHMM COPYRIGHT AND LICENCE
--------------------------------------------------
The Perl Bio::Tools::PSort::ModHMM  module is Copyright (C) 2006
Matthew Laird and Fiona Brinkman.  All rights reserved.

ModHMM is Copyright (C) Hakan Viklund.

This program is licensed under the terms of the Gnu General Public
License.  For more information on the GPL, see the LICENSE file
included with this distribution.


6) AUTHOR INFORMATION
---------------------

The Perl Bio::Tools::PSort::ModHMM module was originally written by
Matthew Laird <matt@sfu.ca> of the Brinkman Laboratory at Simon Fraser
University, Burnaby, BC, Canada.

  http://www.pathogenomics.sfu.ca/brinkman
