The BioJava - Alignment Module
=====================================================

A tutorial for the alignment module of [BioJava](http://www.biojava.org).

## About
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            <img src="img/alignment.png"/>
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            The <i>alignment</i> module of BioJava provides an API that contains
            <ul>
                <li>Implementations of dynamic programming algorithms for sequence alignment</li>
                <li>Reading and Writing of popular alignment file formats</li>
                <li>A single-, or multi- threaded multiple sequence alignment algorithm.</li>
            </ul>

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## Index

This tutorial is split into several chapters.

Chapter 1 - Quick [Installation](installation.md)

Chapter 2 - Global alignment - Needleman and Wunsch algorithm

Chapter 3 - Local alignment - Smith-Waterman algorithm

Chapter 4 - Multiple Sequence alignment

Chapter 5 - Reading and writing of multiple alignments

Chapter 6 - BLAST - why you don't need BioJava for parsing BLAST

## Please cite

**BioJava: an open-source framework for bioinformatics in 2012**<br/>
*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)


## License

The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.

[view license](../license.md)



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