Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. [1] [2] [3] [4] [5] [6]

Please visit the following pages for help: Installation, Getting Started, Running Frealign, Output Files, Classification and Interpreting Results.

The latest version of Frealign is available for download and is subject to Janelia Farm Research Campus Software Copyright 1.1. For support, feedback and bug reports, please use the frealign forum.

A GPU-accelerated version of Frealign (based on version 8.06) was developed by Xueming Li and Yifan Cheng at UCSF and is attached below. It can also be downloaded here (this link also provides information about hardware requirements).

Some scripts are available for converting particle alignment parameters from Spider and Imagic into a Frealign, and from Relion to Frealign. Users of Imagic will be pleased to know that the latest version of Imagic (100818) has conversion routines to convert the alignment parameters from Imagic to Frealign and back.

The development of Frealign began in 1997 at the MRC Laboratory of Molecular Biology in Cambridge, UK with financial support from the MRC and the Deutsche Forschungsgesellschaft. Contributions to the program code were made by:

  • Nikolaus Grigorieff
  • Richard Henderson
  • Christine Villeneuve
  • Matthias Wolf
  • Charles Sindelar
  • Alexis Rohou


Please visit the Frealign documentation pages for help. If you encounter any problems using Frealign, or have questions, please use the frealign forum.