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now with sections for alignment and core modules
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‎.gitignore‎

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.DS_Store
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.profile
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.settings
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.idea

‎README.md‎

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Quick [Installation](installation.md)
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Book 1: [The Protein Structure modules](structure/README.md)
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Book 1: [The Core module](core/README.md), basic working with sequences.
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Book 2: [The Genomics Module](genomics/README.md)
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Book 2: [The Alignment module](alignment/README.md), pairwise and multiple alignments of protein sequences.
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Book 3: Alignments
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Book 3: [The Protein Structure modules](structure/README.md), everything related to working with 3D structures.
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Book 4: [The Genomics Module](genomics/README.md), working with genomic data
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## License

‎alignment/README.md‎

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The BioJava - Alignment Module
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=====================================================
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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/>
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[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
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doi: 10.1093/bioinformatics/bts494
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## License
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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
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[view license](../license.md)
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‎alignment/img/alignment.png‎

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‎alignment/installation.md‎

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## Quick Installation
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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.
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‎core/README.md‎

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The BioJava - Core Module
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=====================================================
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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/>
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[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
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doi: 10.1093/bioinformatics/bts494
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## License
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The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
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[view license](../license.md)
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‎core/img/core.png‎

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‎core/installation.md‎

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## Quick Installation
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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.
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‎genomics/README.md‎

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Chapter 5 - Reading [karyotype (cytoband)](karyotype.md) files
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Chapter 6 - Reading UCSC's .2bit files
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Chapter 6 - Reading genomic DNA sequences using UCSC's [.2bit file format](twobit.md)
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### Author:
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[Andreas Prli&#263;](https://github.com/andreasprlic)
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## Please cite
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**BioJava: an open-source framework for bioinformatics in 2012**<br/>

‎genomics/twobit.md‎

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Reading a .2bit file
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====================
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UCSC's .2bit files provide a compact representation of the DNA sequences for a genome. The TwoBitParser class provides
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the access to the content of this file.
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```java
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File f = new File("/path/to/file.2bit");
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TwoBitParser p = new TwoBitParser(File f);
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String[] names = p.getSequenceNames();
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for(int i=0;i<names.length;i++) {
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p.setCurrentSequence(names[i]);
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p.printFastaSequence();
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p.close();
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}
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```

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