I am not familiar with chromus, but I have never seen any implementation of BLAST that did not test both each sequence and its reverse complement against the query database. As for aligning, the forward sequence does not align to its reverse complement except in the very special case of a palindrome.
Varsha Godbole the thing you want to do it is not called "aligning". I guess you are taking about merging the forward and reverse sequences from sanger sequencing.