Command interpreter: An error checking command interpreter will be used.
Position numbering: Currently, all positions must be referred to in the global coordinate system of the alignment. This is a bit annoying if all your data refer to a specific sequence. I plan to allow residue position numbers to be referred to relative to a specific sequence, or sequences. Similarly, the sequence numbering will be changed to allow a unique numbering scheme that does not change when you insert additional lines in the middle of the alignment.
Command aliasing: This will allow frequently used commands to be renamed to something shorter simplify typing!
Note: In version 1.4.5 part of the position numbering problem is overcome through the use of the program alsnum. See "New features of 1.4.5".