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SUMMARY: Nontargeted LC-MS (liquid chromatography-tandem mass spectrometry) metabolomics datasets contain a wealth of information but present many challenges during analysis and processing. Often, two or more independently processed datasets must be aligned to form a complete dataset, but existing software does not fully meet our needs. For this, we have created an open-source Python package called Eclipse. Eclipse uses a novel graph-based approach to handle complex matching scenarios that arise from n > 2 datasets.AVAILABILITY AND IMPLEMENTATION: Eclipse is open source () and can be installed via "pip install bmxp."