File: README

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alien-hunter 1.7-8
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SUMMARY

alien_hunter is a software for the prediction of Genomic Islands
with the implementation of Interpolated Variable Order Motifs (IVOMs)
capturing sequence compositional biases in various levels (e.g. G+C,
dinucleotide, codon bias). Optionally the predictions can be parsed into
a 2 state 2nd order Hidden Markov Model (HMM) to optimize the predicted
boundaries using a change-point detection framework. Finally the predictions
(embl format) can be automatically loaded into Artemis genome viewer freely
available at: http://www.sanger.ac.uk/Software/Artemis/

RELEASE

The current release is 1.7

INSTALLATION
In order to run alien_hunter, PERL (http://www.perl.com/) and Java Runtime Environment
(http://java.sun.com/) must be already installed. The software has been tested on 
PERL v5.6.1 and JAVA SDK v1.4.2.

After downloading alien_hunter.tar.gz change directory to the directory you wish 
to install alien_hunter in (~/ in this example). Uncompress and untar the 
alien_hunter.tar.gz file. On UNIX the command is: 
gzip -d < alien_hunter.tar.gz | tar xf - 

This will create a directory called ~/alien_hunter which will contain all the 
files necessary for running alien_hunter. 
If JAVA and PERL is correctly setup on your system, type: ./alien_hunter on
the command line to get the manpage of alien_hunter.
To correctly setup your system for the artemis (art) executable visit:
http://www.sanger.ac.uk/Software/Artemis/v8/manual/installation.html and follow
the instructions. If the setup is not proper the "-a" option of alien_hunter will not
work.

(If taken from CVS you should compile the two java files first)

AUTHOR

For questions or comments contact gsv(at)sanger.ac.uk

LICENSE

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.