A command interpreter that does more error checking will be included. Currently, no checking is done to make sure that the correct number of arguments are given to a command.
Sequences will be able to be given unique labels and region commands refer to these labels or ranges of labels. This will permit a sequence to be deleted or added to the alignment without having to update the .als file.
The relative numbering option will be extended to allow numbering relative to a position. e.g. 456+7 would be 7 residues after position 456. This will allow annotation of positions that may be in insertions relative to the reference sequence.
Special TEXT commands will be extended to allow alternative shapes to be drawn and scaled in various ways.
Tree drawing and generalised graphics. An option to draw arbitrary lines on an alignment will be added. This will permit line graphics to be added to an alignment. The initial reason for this will be to show dendrograms (trees) alongside the alignment, but simple line graphs could also be plotted under the alignment.
Fiddle factors will be introduced to allow fine positioning of individual characters. For example, if you like your ``I'' characters to be centred rather than left justified, this will be possible.
In single_pagemode, it will be possible to add arbitrary text to an alignment for final annotation, e.g. titles etc.
Variable height/width sequence lines will be permitted (maybe).