------------------------------------------------------------------------
Since v0.03
DATE: 2007-02-01
Found a small bug with calculating scores.  Alignments should, in
general be of lower RMSD and longer.

------------------------------------------------------------------------
Since v0.02
DATE: 2007-01-31
Found a small bug in sequencing.  Fixed it.

------------------------------------------------------------------------
Since v0.01
DATE: 2007-01-25

CEAlign has the semantic, and syntactic formalism of

 cealign MASTER, TARGET

where a post-condition of the algorithm is that the coordinates of the
'''MASTER''' protein are unchanged.  This allows for easier
multi-protein alignments.  For example,

 cealign 1AUE, 1BZ4
 cealign 1AUE, 1B68
 cealign 1AUE, 1A7V
 cealign 1AUE, 1CPR

will superimpose all the TARGETS onto the MASTER.

