If and only if they are different, then a method taking a database handle should make the necessary changes to the table in question in a transparent manner.
in reply to Automatically altering tables from different schema's
Do you mean you don't want to make the table defintions idenfical if they are already identical? Why not just assume the table definitions are different. Once you have a perl script that can produce the SQL to recreate the table, safe off the data drop table and recreate it and then reload the data.