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<!DOCTYPE html>
<!--
Original Design: Spectral by HTML5 UP
html5up.net | @n33co
Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
Jekyll build mod
-->
<html>
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>BioJava</title>
<meta name="description" content="BioJava is an open-source project
dedicated to providing a Java framework
for processing biological data.
">
<!--[if lte IE 8]><script src="/js/ie/html5shiv.js"></script><![endif]-->
<link rel="canonical" href="http://biojava.org/">
<link rel="stylesheet" href="/css/main.css" />
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<link rel="alternate" type="application/rss+xml" title="BioJava" href="http://biojava.org/feed.xml">
</head>
<body class="landing">
<!-- Page Wrapper -->
<div id="page-wrapper">
<!-- Header -->
<header id="header" class="alt">
<h1><a href="/index.html">BioJava</a></h1>
<nav id="nav">
<ul>
<li class="special">
<a href="#menu" class="menuToggle"><span>Menu</span></a>
<div id="menu">
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="/elements.html">Elements</a></li>
<li><a href="/generic.html">Generic</a></li>
<li><a href="/wiki.html">Wiki Pages</a></li>
<li><a href="#">Sign Up</a></li>
<li><a href="#">Log In</a></li>
<li><a href="/feed.xml"
class="icon fa-feed"> RSS Feed</a></li>
</ul>
</div>
</li>
</ul>
</nav>
</header>
<!-- Banner -->
<section id="banner">
<div class="inner">
<h2>BioJava</h2>
<p><p>BioJava is an open-source project
dedicated to providing a Java framework
for processing biological data.</p>
</p>
<ul class="actions">
<li><a href="https://github.com/biojava/biojava/" class="button special">Get the Source</a></li>
</ul>
</div>
<a href="#one" class="more scrolly">Learn More</a>
</section>
<!-- One -->
<section id="one" class="wrapper style1 special">
<div class="inner">
<header class="major">
<h2>BioJava is open source<br />
</h2>
<p>It's hosted, developed, and maintained on GitHub.<br/>
</p>
<a href="https://github.com/biojava/biojava" class="button big">View the GitHub project</a>
</header>
<ul class="icons major">
<li><span class="icon fa-diamond major style1"><span class="label">Current release: 4.2.0</span></span></li>
<li><span class="icon fa-heart-o major style2"><span class="label">Ipsum</span></span></li>
<li><span class="icon fa-code major style3"><span class="label">Dolor</span></span></li>
</ul>
</div>
</section>
<!-- Two -->
<section id="two" class="wrapper alt style2">
<section class="spotlight">
<div class="image"><img src="images/4hhb.png" alt="" /></div><div class="content">
<h2>Protein Structure Modules<br />
</h2>
<p>provide an API that allow to</p>
<ul>
<li>Maintain local installations of PDB</li>
<li>Load structures and manipulate them</li>
<li>Perform standard analysis such as sequence and structure alignments</li>
<li>Visualize structures</li>
</ul>
</div>
</section>
<section class="spotlight">
<div class="image"><img src="images/1d68.png" alt="" /></div><div class="content">
<h2>Biological Sequences<br />
</h2>
<p>BioJava allows to</p>
<ul>
<li>Perform basic operations on biological sequences</li>
<li>Read and Write popular sequence file formats</li>
<li>Translate DNA sequences into protein sequences</li>
</ul>
</div>
</section>
<section class="spotlight">
<div class="image"><img src="images/1ihm.png" alt="" /></div><div class="content">
<h2>Please cite<br />
</h2>
<p>
<p><strong>BioJava: an open-source framework for bioinformatics in 2012</strong><br />
<em>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</em> <br />
<a href="http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract">Bioinformatics (2012) 28 (20): 2693-2695.</a> <br />
<a href="http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract"><img src="http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat" alt="doi" /></a> <a href="http://www.ncbi.nlm.nih.gov/pubmed/22877863"><img src="http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat" alt="pubmed" /></a></p>
</p>
</div>
</section>
</section>
<!-- Three -->
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<div class="inner">
<header class="major">
<h2>Accumsan mus tortor nunc aliquet</h2>
<p>Aliquam ut ex ut augue consectetur interdum. Donec amet imperdiet eleifend<br />
fringilla tincidunt. Nullam dui leo Aenean mi ligula, rhoncus ullamcorper.</p>
</header>
<ul class="features">
<li class="icon fa-graduation-cap">
<h3>Tutorial</h3>
<p>The <a href="https://github.com/biojava/biojava-tutorial">tutorial</a> offers an introduction into some of the features that are provided by BioJava.</p>
</li>
<li class="icon fa-rocket">
<h3>Cookbook</h3>
<p>The Cookbook provides simple coding recipes that follow a "How do I ..." approach.</p>
</li>
<li class="icon fa-code">
<h3>Javadoc API</h3>
<p>Read the <a href="http://www.biojava.org/docs/api/index.html">Javadoc API</a>.</p>
</li>
<li class="icon fa-globe">
<h3>Current release: 4.2.0</h3>
<p>BioJava is available from Maven Central</p>
</li>
<li class="icon fa-heart-o">
<h3>Aenean Primis</h3>
<p>Augue consectetur sed interdum imperdiet et ipsum. Mauris lorem tincidunt nullam amet leo Aenean ligula consequat consequat.</p>
</li>
<li class="icon fa-flag-o">
<h3>Tortor Ut</h3>
<p>Augue consectetur sed interdum imperdiet et ipsum. Mauris lorem tincidunt nullam amet leo Aenean ligula consequat consequat.</p>
</li>
</ul>
</div>
</section>
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<div class="inner">
<header>
<h2>Arcue ut vel commodo</h2>
<p>Aliquam ut ex ut augue consectetur interdum endrerit imperdiet amet eleifend fringilla.</p>
</header>
<ul class="actions vertical">
<li><a href="#" class="button fit special">Get the Code</a></li>
<li><a href="#" class="button fit">Learn More</a></li>
</ul>
</div>
</section>
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<footer id="footer">
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<li><a target="_blank" href="https://github.com/biojava" class="icon fa-github"
><span class="label">github</span></a></li>
</ul>
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<li>©
2000,
2016
BioJava</li>
<li>Design: <a href="http://html5up.net" target="_blank">HTML5 UP</a></li>
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