Here is an updated summary of methods in Bio::Align.
When defining a method in the package, several things need to be considered:
2. Return value
3. Whether to change the object calling the method
4. backward compatibility
So the summary is given by these attributes. It is not really human readable at the moment, but it will be the base of the new HOWTO of Bio::Align
Now, most of the new proposed methods are finished. By 22/06, all the new methods will be finished, thus reach the first milestone.