== Aligners ==

To get a current list of Aligners, run '''''e2help.py aligner''''' or for more detailed information '''''e2help.py aligner -v 2'''''.

For single particle analysis, we currently recommend using ''rotate_translate_flip'' for first stage alignment, and ''refine'' for second-stage alignment. ''refine'' is currently the only available 2-D second stage aligner.

The ''_3d'' variants are for Single Particle Tomography or other 3-D alignment tasks.