Imalign for a few images:

        input = "procc5m.imh,procd5m.imh" Input images
    reference = "procc5m.imh"   Reference image
       coords = "refcoords"     Reference coordinates file
       output = "shiftc5m.imh,shiftd5m.imh" Output images
      (shifts = "")             Initial shifts file
     (boxsize = 7)              Size of the small centering box
      (bigbox = 23)             Size of the big centering box
    (negative = no)             Are the features negative ?
  (background = INDEF)          Reference background level
       (lower = INDEF)          Lower threshold for data
       (upper = INDEF)          Upper threshold for data
    (niterate = 3)              Maximum number of iterations
   (tolerance = 0)              Tolerance for convergence
 (shiftimages = yes)            Shift the images ?
 (interp_type = "linear")       Interpolant
(boundary_typ = "nearest")      Boundary type
    (constant = 0.)             Constant for constant boundary extension
  (trimimages = yes)            Trim the shifted images ?
     (verbose = yes)            Print the centers, shifts, and trim section ?
        (list = "")             
        (mode = "ql")           


Imalign for many images (for the example of 120sec exposures): 

        input = "@in120list"    Input images
    reference = "procc5m.imh"   Reference image
       coords = "refcoords"     Reference coordinates file
       output = "@out120list"   Output images
      (shifts = "")             Initial shifts file
     (boxsize = 7)              Size of the small centering box
      (bigbox = 23)             Size of the big centering box
    (negative = no)             Are the features negative ?
  (background = INDEF)          Reference background level
       (lower = INDEF)          Lower threshold for data
       (upper = INDEF)          Upper threshold for data
    (niterate = 3)              Maximum number of iterations
   (tolerance = 0)              Tolerance for convergence
 (shiftimages = yes)            Shift the images ?
 (interp_type = "linear")       Interpolant
(boundary_typ = "nearest")      Boundary type
    (constant = 0.)             Constant for constant boundary extension
  (trimimages = yes)            Trim the shifted images ?
     (verbose = yes)            Print the centers, shifts, and trim section ?
        (list = "")             
        (mode = "ql")