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Small fixes to the main webpage
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‎_config.yml‎

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# Site settings
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title: BioJava
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description: |
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BioJava is an open-source project
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dedicated to providing a Java framework
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for processing biological data.
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description: The open-source Java framework for bioinformatics
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owner: BioJava
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first_published: 2000
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email: biojava-l@biojava.org

‎index.html‎

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<section id="banner">
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<div class="inner">
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<h2>{{ site.title }}</h2>
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<p>{{ site.description | markdownify }}</p>
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<p>{{ site.description | markdownify }}</p><br>
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<ul class="actions">
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<li><a href="https://github.com/biojava/biojava/" class="button special">Get the Source</a></li>
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<li><a href="wiki/BioJava%3AGetStarted" class="button special">Get started</a></li>
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</ul>
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</div>
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<a href="#one" class="more scrolly">Learn More</a>
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<section id="one" class="wrapper style1 special">
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<div class="inner">
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<header class="major">
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<h2>BioJava is open source<br />
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</h2>
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<p>It's hosted, developed, and maintained on GitHub.<br/>
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</p>
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<a href="https://github.com/biojava/biojava" class="button big">View the GitHub project</a>
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<h2>Open source</h2>
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<p>The project is hosted, developed, and maintained on GitHub.</p>
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<a href="https://github.com/biojava/biojava" class="button big">GitHub project</a>
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</header>
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<ul class="icons major">
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<li><span class="icon fa-diamond major style1"><span class="label">Current release: {{ site.release.version }}</span></span></li>
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<li><span class="icon fa-heart-o major style2"><span class="label">Ipsum</span></span></li>
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<li><span class="icon fa-code major style3"><span class="label">Dolor</span></span></li>
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</ul>
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</div>
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</section>
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<!-- Two -->
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<section id="two" class="wrapper alt style2">
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<section class="spotlight">
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<div class="image"><img src="images/4hhb.png" alt="" /></div><div class="content">
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<h2>Protein Structure Modules<br />
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</h2>
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<p>provide an API that allow to</p>
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<ul>
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<li>Maintain local installations of PDB</li>
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<li>Load structures and manipulate them</li>
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<li>Perform standard analysis such as sequence and structure alignments</li>
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<li>Visualize structures</li>
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</ul>
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<h2>Protein structures</h2>
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<p>BioJava provides an API to maintain local installations of the PDB, load and manipulate structures, perform standard analysis such as sequence and structure alignments and visualize them in 3D.</p>
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</div>
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</section>
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<section class="spotlight">
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<div class="image"><img src="images/1d68.png" alt="" /></div><div class="content">
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<h2>Biological Sequences<br />
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</h2>
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<p>BioJava allows to</p>
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<ul>
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<li>Perform basic operations on biological sequences</li>
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<li>Read and Write 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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<h2>Biological sequences</h2>
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<p>BioJava supports reading and writing popular sequence file formats, translating DNA sequences into proteins and other common bioinformatics routines.</p>
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</div>
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</section>
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<section class="spotlight">
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<div class="image"><img src="images/1ihm.png" alt="" /></div><div class="content">
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<h2>Please cite<br />
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</h2>
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<p>
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{% capture my-citation %}{% include citation.md %}{% endcapture %}
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{% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
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{{ my-citation | markdownify }}
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</p>
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</div>
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</section>
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</section>
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<section id="three" class="wrapper style1 special">
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<div class="inner">
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<header class="major">
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<h2>Mailing list</h2>
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<h2>Get in touch</h2>
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<p>
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Questions, comments, and communications regarding BioJava can be made either on github or on the BioJava mailing list:
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Questions, comments, and communications regarding BioJava can be done either on <a href="https://github.com/biojava/biojava/issues">
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<span class="label">GitHub</span></a> or through the <a href="http://lists.open-bio.org/mailman/listinfo/biojava-l">
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<span class="label">BioJava mailing list</span></a>. Subscribe to stay up to date!
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</p>
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</header>
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<ul class="icons major">
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<li><span class="icon fa-envelope-o major style1"></span>
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<a href="/wiki/BioJava:MailingLists/">
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<span class="label">biojava-l</span>
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</a> general discussion list
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</li>
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</ul>
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<li><span class="icon fa-envelope-o major style1"></span></li>
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<li><span class="icon fa-heart-o major style2"></span></li>
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<li><span class="icon fa-code major style3"></span></li>
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</ul>
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</div>
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</section>
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<ul class="features">
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<li class="icon fa-graduation-cap">
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<h3>Tutorial</h3>
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<p>The tutorial offers an introduction into some of the features that are provided by BioJava.</p>
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<a href="https://github.com/biojava/biojava-tutorial" class="button">tutorial</a>
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<p>The tutorial offers an introduction into some of the features provided by BioJava.</p>
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<a href="https://github.com/biojava/biojava-tutorial" class="button">Tutorial</a>
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</li>
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<li class="icon fa-rocket">
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<h3>Cookbook</h3>
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<p>The Cookbook provides simple coding recipes that follow a "How do I ..." approach.</p>
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<a href="http://biojava.org/wiki/BioJava:CookBook4.0/" class="button">Cookbook</a>
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<h3>CookBook</h3>
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<p>The Cookbook provides simple coding recipes to common bioinformatics problems using BioJava.</p>
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<a href="wiki/BioJava%3ACookBook4.0" class="button">Cookbook</a>
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</li>
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<li class="icon fa-code">
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<h3>Javadoc API</h3>
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<p>The Javadocs for the current BioJava release</p>
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<p>The Javadocs for the current BioJava {{site.release.version}} release.</p>
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<a href="docs/api" class="button">Javadoc API</a></br>
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</li>
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<li class="icon fa-globe">
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<h3>Current release: {{ site.release.version }}</h3>
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<p>BioJava is available from Maven Central</p>
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<h3>Release {{ site.release.version }}</h3>
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<p>BioJava is available from Maven Central.</p>
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<a href="https://mvnrepository.com/artifact/org.biojava" class="button">Maven Central</a></br>
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</li>
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<li class="icon fa-heart-o">
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<h3>Wiki</h3>
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</li>
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<li class="icon fa-flag-o">
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<h3>Legacy Javadoc API</h3>
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<p>The Javadocs for legacy 1.x BioJava.</p>
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<p>The Javadocs for BioJava legacy 1.x versions.</p>
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<a href="docs/api1.9.1/" class="button">View 1.9.1 API</a>
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</li>
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</ul>
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<section id="cta" class="wrapper style4">
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<div class="inner">
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<header>
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<h2><img src="/images/logo/logo_favicon_65.png" style="vertical-align:middle"/> Learn More</h2>
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<p>Here a couple of pointers for how to get started</p>
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<h2><img src="/images/logo/logo_favicon_250.png" height="60" style="vertical-align:middle"/> Learn More</h2>
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<p>Here a couple of pointers to get you started</p>
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</header>
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<ul class="actions vertical">
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<li><a href="wiki/Get_source/" class="button fit special">Get the Code</a></li>
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<li><a href="wiki/BioJava:GetStarted/" class="button fit">Get Started</a></li>
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<li><a href="wiki/BioJava%3AGetStarted" class="button fit special">Get started</a></li>
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<li><a href="https://github.com/biojava/biojava" class="button fit">Get the source</a></li>
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</ul>
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</div>
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</section>

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