User's Guide for OrthoGNC version 1.5 

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================== About ==========================
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OrthoGNC is a software for predicting accurate pairwise orthology relations 
based on gene neighborhood conservation. 

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================ Requirements =====================
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(1) To run OrthoGNC you need to install NCBI BLAST+. 
  - The latest BLAST+ package is available at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
  - We have tested OrthoGNC with BLAST version 2.4.0+, however, it should work with newer versions.
  
(2) OrthoGNC is developed with Java and needs JRE to run.
  - The latest JRE is available at http://www.oracle.com/technetwork/java/javase/downloads/index.html

(3) OrthoGNC works both on MS Windows and Linux. It is tested on  MS Windows 10(64bit) 
	and Linux Mint 17.3 Cinnamon(64bit).

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============== Files and Folders ==================
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(1) config.txt
  - This file contains the user defined parameters. Change the parameters to your desired valuse. 
    The file is very easy to read and self-explanatory.
  
(2) OrthoGNC.jar
  - This is the OrthoGNC binary file.

(3) testproject (folder)
  - This folder contains 3 sample species for test purposes.

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================ Runing OrthoGNC ==================
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To run the project from command line, go to the binary folder and type the following command:

java -jar "OrthoGNC.jar" 

OrthoGNC automatically reads the user defined parameters from config.txt file.

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========== Output Files and Folders ===============
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After Running OrthoGNC the following files and folders will be created:

(1) "/result" folder
  - This folder contains the working directories. For each project a seperate folder 
	will be created and named after the project name.

(2) "/result/'ProjectName'" folder
  - This folder will be created for each project.
	
(3) "/result/'ProjectName'/blast_results" folder
  - This folder contains the BLAST results for the current project. For each e-value a 
	seprate folder will be created. By saving BLAST results OrthoGNC is capable of skipping 
	the BLAST step. This improves the running time considerably. If you wish to force 
	OrthoGNC to do the BLAST queries please delete this folder manually.
  
(4) "/result/'ProjectName'/output" folder
  - This folder contains the final output of OrthoGNC. A text file containing the pairwise 
	orthology relations will be created. The file names summarizes the input parameters.
	For exmple a sample output file is "Output_Intersection_1e-2_30.0_50.0_7_9_0.8.txt" which
	means OrthoGNC have used the following parameters:
	NIR=UniqueIntersection
	Evalue=1e-2
	T_i=30
	T_c=50
	N=7
	T_n=9
	T_b=0.8
===================================================
=================== Contact =======================
===================================================

Please contact s(dot)jahangiri(dot)cs(at sign)gmail.com if you have any questions.

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=============== Software License ==================
===================================================
The OrthoGNC Software is Copyright 2010 by the Eslahchi-Lab.

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/>.