homologhmm
A hidden Markov Model sequence and alignment decoder 

(c) 2005 Lukas Kall.

The program is distributed under GPL, see http://gnu.org for details
The program uses the BioJava (http://biojava.org) which is distributed under LGPL

and 

jPhobius a java implementation of Phobius
a hidden Markov Model capable of predicting both Transmembrane Topology
and Signal peptides

(c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer.

Please cite:

    Lukas Käll, Anders Krogh and Erik Sonnhammer.
    An HMM posterior decoder for sequence feature prediction that includes homology information
    Bioinformatics, 21 (Suppl 1):i251-i257, June 2005.

or

    Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer.
    A Combined Transmembrane Topology and Signal Peptide Prediction Method.
    Journal of Molecular Biology, 338(5):1027-1036, May 2004.



PREREQUISITES
=============

Unix/Linux
Perl 5.6 or later
Java 1.5.0 or later
To retrieve homologs with the script blastget BioPerl(bioperl.org) is needed.
If jPhobius is to be used: The phobius.model file from your licensed copy of
phobius 

    
INSTALL
=======

Change (and create) directory to the directory where you want to install homologhmm
(e.g. /usr/local/share/jphobius ), and unpack the tar file with the command:

cat /path_to_tarfile/jphobius.tar.gz | tar xz

make a link from the file jphobius and homologhmm to a directory included in your standard
path.

ln -s /usr/local/share/jphobius/jphobius /usr/local/bin/phobius
ln -s /usr/local/share/jphobius/homologhmm /usr/local/bin/homologhmm

Make sure that java is available in the standard path

NOTE: To vitalize jPhobius please copy the file phobius model into 
the homologhmm directory (/usr/local/share/jphobius)