# ##############################################################################
# NLStradamus FOR DISTRIBUTION
# Copyright Alex Nguyen Ba 2012
#
# LICENCE 
#
#    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 3 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, see <http://www.gnu.org/licenses/>.

# ##############################################################################

README file

The use of this text file is to provide the user with basic usage of the 
standalone of NLStradamus.

BASIC INSTALLATION

The user should be familiar with running PERL scripts and place the 
nlstradamus.pl file within an accessible folder. Place a .fasta file of your
proteins of interests in the same folder.

BASIC USAGE

A list of helpful commands can be accessed by typing :
perl nlstradamus.pl -help

A list of arguments used by NLStradamus can be viewed under the -help command,
only one of them being mandatory. 

-i followed by your input file, which is the .fasta file of your proteins of 
interest. An example of this : 

perl nlstradamus.pl -i orf_trans.fasta

This will run NLStradamus on the proteins in orf_trans.fasta

-t sets the posterior threshold. The default value of this parameter is 0.6,
but can be set to any value between 0 and 1. The posterior threshold is the 
statistical threshold where the posterior probability should be counted as a
positive hit. An example of this : 

perl nlstradamus.pl -i orf_trans.fasta -t 0.7

-m sets the model. The default value of this parameter is 1, which is the
two-state model. This value can take a value of 1 or 2, 2 being the four-state
bipartite model. An example of this : 

perl nlstradamus.pl -i orf_trans.fasta -t 0.5 -m 2

The default values are set to the maximal values given by a ROC curve.

OUTPUT

The output of NLStradamus contains the gene ID followed by the predicted sequences.

The graphics and the tables are not output by the PERL script, but are available
online. 


