Update README.md

Use massage with examples

Author: hani-girgis

README.md

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 # Identity
 
-Academic use: Affero general public license version 1.
+Identity 1.0 is developed by Hani Z. Girgis, PhD.
 
-Any restrictions to use for-profit or non-academics: Alternative commercial license is needed; please contact Dr. Hani Z. Girgis (hzgirgis at buffalo dot edu) for more information.
+This program calculates DNA sequence identity scores rapidly without alignment.
+
+Copyright (C) 2020 Hani Z. Girgis, PhD
+
+Academic use: Affero General Public License version 1.
+
+Any restrictions to use for profit or non-academics: Alternative commercial license is required.
+
+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.
+
+Please contact Dr. Hani Z. Girgis (hzgirgis@buffalo.edu) if you need more information.
+
+Please cite the following paper: 
+	Identity: Rapid alignment-free prediction of sequence alignment identity scores using
+	self-supervised general linear models. Hani Z. Girgis, Benjamin T. James, and Brian B.
+	Luczak. NAR GAB, 2020.
+
+List of parameters:
+	-d: Required. Database file in FASTA format.
+	-o: Required. Output file.
+	-t: Required. Identity score threshold (between 0 & 0.99), below which pairs are not reported.
+	-q: Optional. Query file in FASTA format. If no query(s) is provided, all versus all is
+	    performed on the database file.
+	-c: Optional. Number of cores or hyperthreads. For the search mode, set this parameter to the
+	    number of cores not hyperthreads. For example, suppose your computer has 4 cores, each of
+	    which supports 2 hyperthreads. Set this parameter to 4 if you are using the search mode or
+	    to 8 if you are using the all-versus-all mode. By default, all hyperthreads are used.
+	-r: Optional. Automatically relax the threshold according to the predictor error -- y (yes) or
+	    n (no). By default, it is enabled except if the threshold is 0.9 or higher.
+	-l: Optional. Print academic license (Affero General Public License version 1) and exit -- y
+	    (yes) or n (no).
+	-h: Optional. Print this help message.
+
+Examples: 
+	1. To perform database search with a minimum identity score of 0.7
+		identity -d databas.fasta -q query.fasta -o output.txt -t 0.7
+
+	2. To perform database search with a minimum identity score of 0.7 using 10 threads
+		identity -d databas.fasta -q query.fasta -o output.txt -t 0.7 -c 10
+
+	3. To perform all versus all with a minimum identity score of 0.8
+		identity -d databas.fasta -o output.txt -t 0.8
+
+	4. To perform all versus all with a minimum identity score of 0.8 with strict threshold
+		identity -d databas.fasta -o output.txt -t 0.8 -r n
+
+	5. To print the academic lincense
+		identity -l y