ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data

•ContinuousFlex helps analyzing continuous macromolecular conformational variability.•It can be used with single particle and tomography data (in vitro and in situ).•It is user-friendly open-source software available as a plugin for Scipion.•It combines image processing, simulation, deep learning, and statistical analysis.