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A tutorial for the alignment module of [BioJava](http://www.biojava.org).
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## About
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<table>
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<tr>
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<td>
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<img src="img/alignment.png"/>
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</td>
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<td>
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The <i>alignment</i> module of BioJava provides an API that contains
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<ul>
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<li>Implementations of dynamic programming algorithms for sequence alignment</li>
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<li>Reading and Writing of popular alignment file formats</li>
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<li>A single-, or multi- threaded multiple sequence alignment algorithm.</li>
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</ul>
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</td>
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</tr>
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</table>
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## Index
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This tutorial is split into several chapters.
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Chapter 1 - Quick [Installation](installation.md)
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Chapter 2 - Global alignment - Needleman and Wunsch algorithm
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Chapter 3 - Local alignment - Smith-Waterman algorithm
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Chapter 4 - Multiple Sequence alignment
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Chapter 5 - Reading and writing of multiple alignments
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Chapter 6 - BLAST - why you don't need BioJava for parsing BLAST
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## Please cite
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**BioJava: an open-source framework for bioinformatics in 2012**<br/>
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*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/>
In the beginning, just one quick paragraph of how to get access to BioJava.
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BioJava is open source and you can get the code from [Github](https://github.com/biojava/biojava), however it might be easier this way:
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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```xml
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<dependencies>
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...
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<!-- This imports the latest version of BioJava core module -->
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-core</artifactId>
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<version>3.0.8</version>
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</dependency>
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<!-- other biojava jars as needed -->
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</dependencies>
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```
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If you run
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<pre>
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mvn package
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</pre>
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on your project, the BioJava dependencies will be automatically downloaded and installed for you.
A tutorial for the core module of [BioJava](http://www.biojava.org).
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## About
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<table>
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<tr>
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<td>
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<img src="img/core.png"/>
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</td>
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<td>
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The <i>core</i> module of BioJava provides an API that provides
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<ul>
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<li>Basic operations with biological sequences</li>
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<li>Reading and Writing of popular sequence file formats</li>
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<li>Translate DNA sequences into protein sequences</li>
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</ul>
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</td>
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</tr>
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</table>
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## Index
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This tutorial is split into several chapters.
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Chapter 1 - Quick [Installation](installation.md)
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Chapter 2 - Reading and Writing of FASTA sequences
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Chapter 3 - Translating DNA and protein sequences.
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## Please cite
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**BioJava: an open-source framework for bioinformatics in 2012**<br/>
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*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/>
In the beginning, just one quick paragraph of how to get access to BioJava.
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+
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+
BioJava is open source and you can get the code from [Github](https://github.com/biojava/biojava), however it might be easier this way:
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+
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+
BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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+
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+
Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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+
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+
You can add the BioJava repository by adding the following XML to your project pom.xml file:
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+
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```xml
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<repositories>
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+
...
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+
<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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```xml
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<dependencies>
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+
...
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<!-- This imports the latest version of BioJava core module -->
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-core</artifactId>
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<version>3.0.8</version>
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</dependency>
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<!-- other biojava jars as needed -->
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</dependencies>
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```
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If you run
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<pre>
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mvn package
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</pre>
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on your project, the BioJava dependencies will be automatically downloaded and installed for you.
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