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moving link to Strap from Cookbook to here
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_wikis/BioJava:BioJavaInside.md

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- [MassSieve](http://www.proteomecommons.org/dev/masssieve/index.html):
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An open source application to analyze mass spec proteomics data.
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- [Strap](http://www.charite.de/bioinf/strap/): A tool for multiple
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sequence alignment and sequence based structure alignment.
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Publications
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_wikis/BioJava:BioJavaInside.mediawiki

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* [http://www.proteomecommons.org/dev/masssieve/index.html MassSieve]: An open source application to analyze mass spec proteomics data.
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* [http://www.charite.de/bioinf/strap/ Strap]: A tool for multiple sequence alignment and sequence based structure alignment.
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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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