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.