The following dataset embeds two known structures that have been aligned using a struture alignment package (ref_aln.aln). Using this reference alignment, try to produce with Expresso an alignment as accurate as possible. In theory, you should be able to reach a very high accuracy (~90%) provided you use the right parameters, and the right templates.

You can evaluate the accuracy of any alignment with the following command:
t_coffee -other_pg aln_compare -al1 ref_aln.aln -al2 [your aln]