===== 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.