TMHMM2.0c

The TMHMM package is obtained from
	Anders Krogh, krogh@cbs.dtu.dk

       ******   PLEASE DO NOT REDISTRIBUTE THE PACKAGE   ******


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 author 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.


TMHMM is described in

Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer:
Predicting Transmembrane Protein Topology with a Hidden Markov
Model: Application to Complete Genomes.
J. Mol. Biol. 305:567-580, 2001.

and

Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh:
A hidden Markov model for predicting transmembrane helices in protein
sequences.
In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent
Systems for Molecular Biology, pages 175-182. AAAI Press, 1998.



DEPENDENCIES:
=============

You need an executable of the program decodeanhmm that runs under
Unix. The program may already be in bin/decodeanhmm.

The scripts require perl 5.x

For plotting gnuplot is needed (making postscript plots).

When generating html output the postscript plots are converted to
gif, and for this you need the programs ghostscript (gs) and ppmtogif.


INSTALLATION:
=============

The package is packed with tar and possibly compressed (gzip).

It unpacks in a directory called TMHMM2.0a

The directory contains these files:

        README               This file
	TMHMM2.0.html        TMHMM user's guide
	bin/decodeanhmm      Binary executable
	bin/tmhmm            a perl script to run the program
	bin/tmhmmformat.pl   a perl script used by tmhmm
	lib/TMHMM1.0.model   Model used in version one (used with tmhmm -v1)
	lib/TMHMM2.0.model   Default model
	lib/TMHMM2.0.options File containing options for TMHMM


After unpacking the directory you should

1. Insert the correct path for perl 5.x in the first line of the scripts
   bin/tmhmm and bin/tmhmmformat.pl (if not /usr/local/bin/perl).
2. Make sure you have an executable version of decodeanhmm in the bin
   directory.
3. Include the directory containing tmhmm in your path.
4. Read the TMHMM2.0.guide.html.
5. Run the program.


Anders Krogh
krogh@cbs.dtu.dk
