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

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

## About
<table>
    <tr>
        <td>
            <img src="img/alignment.png"/>
        </td>
        <td>
            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>
        </td>
    </tr>
</table>   

## 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](smithwaterman.md) - 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

## License

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

## Please cite

**BioJava 5: A community driven open-source bioinformatics library**<br/>
*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)



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