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The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.
LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal.
!!!!!! PROJECT MOVED TO GITHUB !!!!!!
Please check out http://raphaelbauer.github.io/lajolla/