Algorithm::HMM 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
--------------

Algorithm::HMM was originally written by Cory Spencer of the Simon Fraser
University Brinkman Laboratory and provides Perl bindings for a Hidden
Markov Model.  It is currently maintained by Matthew Laird and all
inquiries, patches and comments should be sent to him.

Algorithm::HMM is based on the HMMER distribution developed at
Washington University in St. Louis.  For more information on HMMER,
see the project homepage at:

  http://hmmer.wustl.edu/

To read about the latest features, see the Changes file.

The author invites feedback on Algorithm::HMM. If you find a bug, please send the
information described in the BUGS section below.


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

Algorithm::HMM has been tested under linux/x86, linux/i64,
other operating systems are not supported at this time.  However if you
require Algorithm::HMM 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.i64
For OS X installation instructions please see README.osx
For Solaris installation instructions please see README.solaris

Before installation, you will need to compile the libhmmer and
libsquid libraries.  All the required source files for these libraries
are contained in the src/hmmer and src/squid directories.  The
libraries can be compiled as follows:

  cd src/hmmer/
  make
  cp libhmmer.so /usr/local/lib

  cd ../squid/
  make
  cp libsquid.so /usr/local/lib

  ldconfig

Installation of the Algorithm::HMM module is then as follows:

   perl Makefile.PL
   make
   make test
   make install


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

Algorithm::HMM does requires the libhmmer and libsquid libraries to be
compiled and installed.  Both libraries are distributed with this
module.

Currently, this module only supports loading and saving modules
previously created with the HMMER distribution.  If you need to create
new models, you will have to download and install the HMMER programs
from the HMMER homepage.


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 Algorithm::HMM
    * 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) Algorithm::HMM COPYRIGHT AND LICENCE
---------------------------------------
The Perl Algorithm::HMM module is Copyright (C) 2002 Cory Spencer and 
Fiona Brinkman.  All rights reserved.

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 Algorithm::HMM module was originally written by Cory Spencer but is
currently maintained by Matthew Laird <matt@brinkman.mbb.sfu.ca> of the
Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada.

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

Any questions related to the underlying HMMER libraries should be directed 
to the authors of the HMMer package.  The HMMER homepage is currently located at:

  http://hmmer.wustl.edu/


