AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction

•AreTomo, a GPU accelerated software package, fully automates motion-corrected marker-free tomographic alignment and reconstruction.•AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging.•AreTomo enables the on-the-fly reconstruction of tomograms in parallel with tilt series collection, thus providing users with real-time feedback of sample quality.