Appion

to run:

1) run alignment
2) select "Xmipp Clustering 2D Alignment"
3) choose stack, set # particles to some small number
4) set number of references to something small, e.g. 4
5) set number of iterations to something small, e.g. 10
6) run
7) drink a beer
8) complain to Dmitry if something isn't working