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added GenBeans
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_wikis/BioJava:BioJavaInside.md

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thousands of structures. Including an easy to use command line
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interface. Open source at Sourceforge.
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- [GenBeans](http://www.geneinfinity.org/genbeans/index.html): A rich
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client platform for bioinformatics primarily focused on molecular
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biology and sequence analysis.
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Publications
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_wikis/BioJava:BioJavaInside.mediawiki

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* [http://lajolla.sourceforge.net LaJolla] Structural alignment of RNA and proteins using an index structure for fast alignment of thousands of structures. Including an easy to use command line interface. Open source at Sourceforge.
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* [http://www.geneinfinity.org/genbeans/index.html GenBeans]: A rich client platform for bioinformatics primarily focused on molecular biology and sequence analysis.
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== Publications ==
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BioJava has been used in the following publications. If you know of other publications please add them.
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