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**DIAMOND v0.7.4 by Benjamin Buchfink** - http://github.com/bbuchfink/diamond
**DIAMOND v0.7.5 by Benjamin Buchfink** - http://github.com/bbuchfink/diamond

Published in *Nature Methods* **12**, 59–60 (2015) | `doi:10.1038/nmeth.3176 <http://dx.doi.org/10.1038/nmeth.3176>`_

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

Download & Installation
=======================
DIAMOND runs on Linux operating systems and can be downloaded in binary format for immediate use::
If you use a recent **Linux** operating system, you can download the software in binary format for immediate use::

wget http://github.com/bbuchfink/diamond/releases/download/v0.7.4/diamond-linux64.tar.gz
wget http://github.com/bbuchfink/diamond/releases/download/v0.7.5/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz

Alternatively, the software can be compiled from source (see `Compiling from source`_).
Users of **Mac OS X** and some **old Linux systems** need to compile the software from source (see `Compiling from source`_).

Basic command line use
======================
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To compile DIAMOND from source, invoke the following commands on the shell::

$ wget http://github.com/bbuchfink/diamond/archive/v0.7.4.tar.gz
$ tar xzf v0.7.4.tar.gz
$ cd diamond-0.7.4/src
$ wget http://github.com/bbuchfink/diamond/archive/v0.7.5.tar.gz
$ tar xzf v0.7.5.tar.gz
$ cd diamond-0.7.5/src
$ ./install-boost # optional, for installing Boost
$ make
The diamond binary will be created in ``diamond-0.7.4/bin``.
The diamond binary will be created in ``diamond-0.7.5/bin``.

Scoring matrices
================
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