In EMAN2, e2refine2d.py will compute and save Eigenimages from the aligned particle stack in each iteration as r2d_01/basis_XX.hdf

http://eman2.org/Programs/e2refine2d
or 
e2refine2d.py --help

alternatively, if you want to just use a single alignment reference then compute Eigenimages:

e2a2d_align.py ptclstack.hdf align_ref.hdf,3 --threads=8 --saveali

where ptclstack.hdf contains the phase-flipped particle stack (note that you may still get Eigenimages related to defocus differences),
align_ref.hdf is a particle stack (or single image) containing the alignment reference and "3" is the image number to use as a reference (0 is the first image),
--threads is the number of cores on the machine

e2msa.py m2d_01/aliptcls_01.hdf basis.hdf --nbasis 12
will compute the first 12 Eigenimages and save them in basis.hdf

As with other EMAN2 programs you can use any file format you prefer for input...

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <[log in to unmask]>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)



On May 13, 2018, at 8:32 PM, Yangqi Gu <[log in to unmask]> wrote:

Hi all,
I am trying to compute the eigenimages of my particles and first I think I need to align my particles. Does anyone know which software will be the best to do the alignment? My particles are segmented helices and I do have some 2D class averages.
Best,
Yangqi