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PyTom provides the essential tools for the analysis of subtomograms obtained by cryo electron tomography. It covers a processing pipeline of tomogram reconstruction, localization of macromolecular complexes in tomograms, fine alignment of subtomograms extracted at these locations and their classification. PyTom is mostly written in Python making it fairly easy to add new functionality as well as to customize existing methods for specific purposes. The package is mainly developed in the Förster lab at Utrecht University (previously Max Planck Institute for Biochemistry), but we highly encourage developers to contribute to PyTom on an open source basis.