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README.md

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-Amordad
-=======
+# Amordad
 
-Amordad
+## Introduction
+Amordad is an efficient database engine for alignment-free, content-based indexing of metagenomic datasets.
+Amordad places the metagenome comparison problem in a geometric
+context, and uses an indexing strategy that combines random hashing
+with a regular nearest neighbor graph. This framework allows refinement
+of the database over time by continual application of random
+hash functions, with the effect of each hash function encoded in the
+nearest neighbor graph. This eliminates the need to explicitly maintain
+the hash functions in order for query efficiency to benefit from the
+accumulated randomness. Results on real and simulated data show
+that Amordad can support logarithmic query time for identifying similar
+metagenomes even as the database size reaches into the millions.
+
+## Contacts and bug reports
+Andrew D. Smith
+[email protected]
+
+Ehsan Behnam
+[email protected]
+
+Wenzheng Li
+[email protected]
+
+If you found a bug or mistake in this project, we would like to know about it. Before you send us the bug report though, please check the following:
+
+1. Are you using the latest version? The bug you found may already have been fixed.
+2. Check that your input is in the correct format and you have selected the correct options.
+3. Please reduce your input to the smallest possible size that still produces the bug; we will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be.
+
+## LICENSE
+The Amordad database engine for metagenomics Copyright (C) 2014 Andrew D Smith, Ehsan Behnam, Wenzheng Li, and the University of Southern California
+
+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/.