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Features:

The Findall menu can be customized to search for sequences that are used often, i.e. primers like M13, T7
or any sequence that you repeatedly need to look for.

Update ReadSeq so that names in the PAUP/Nexus format can be up to 25 characters long.
ReadSeq now recognizes - . _ symbols in sequence names for NEXUS format.
Also, updated Nexus header so interleave=yes, missing=? and gap=-.

Yanking (Fetching) command "control-k or control-l" will use the repeat feature.
The repeat feature is the ability to type "10" and hit either the spacebar to insert 10 spaces into a sequence,
or hit the delete key and delete 10 characters. The yanking feature which pulls a base from either the right or left
also uses this and preserves any gap alignment. Example: place the insert point where you want to yank to,
then type the number 50. Now push the control key and either k (left) or l (right) and 50 characters, including gaps,
will move to the new position. Again, this will preserve the alignment.

The three button Unix mouse is emulated in X11.app as follows:
Click = Left
Command(Apple key)+Click = Right
Option+Click = Middle

Keyboard shortcuts (Meta Keys): The following meta (=Command/Apple) keys work in MacGDE, BUT only once a sequence has been opened:

command (apple) + shift cursor over sequence names (left panel) + spacebar --> New empty MacGDE window

command (apple) + shift cursor over sequences (right panel) + A --> Opens the Find All window
command (apple) + shift cursor over sequences (right panel) + C --> Applies the Alignment Color mask
command (apple) + shift cursor over sequences (right panel) + D --> Opens the Display Properties panel
command (apple) + shift cursor over sequences (right panel) + G --> Groups sequences selected in the left panel
command (apple) + shift cursor over sequences (right panel) + H --> Opens the Help window
command (apple) + shift cursor over sequences (right panel) + I --> Opens the Get info window
command (apple) + shift cursor over sequences (right panel) + K --> Change Case
command (apple) + shift cursor over sequences (right panel) + N --> Opens New Sequence entry panel
command (apple) + shift cursor over sequences (right panel) + P --> Opens the Protections panel
command (apple) + shift cursor over sequences (right panel) + S --> Saves the File with a Backup file
command (apple) + shift cursor over sequences (right panel) + U --> Ungroups sequences selected in the left panel

command (apple) + cursor over sequences (right panel) + q --> Quits and deletes Backup file
command (apple) + cursor over sequences (right panel) + c --> copies sequence(s) in the left panel to clipboard
command (apple) + cursor over sequences (right panel) + v --> paste clipboard contents below selected sequence in the left panel
command (apple) + cursor over sequences (right panel) + x --> cuts sequence(s) selected in the left panel to clipboard

Within the sequence alignment window the large Delete (Backspace) key above the Return key will not delete sequence.
So if you are on an extended keyboard use the small Del key under the help button, or if you don't have this button
hold down the Control key then hit the large Delete (Backspace) key.

The Complement button under the DNA/RNA menu has been moved down to the second position
The first button is now Alignment Color Mask, see above.

Bugs:

This bug seems to be present in GDE running on all platforms. It has to do with the Mask, if you do not know
what the mask is or how to use it go to page 7 in the Manual. When you mask a sequence the first character in the mask
needs to be a "1" otherwise the mask seems to skip the first 20 or so bases that SHOULD be included in the analysis.
You can make the first character in your alignment a - or N if you are not starting with the first character in your alignment.

Save as.., Import Foreign Format... and the Open... commands seem to be dealing with spaces in names correctly, though an error will appear in the xterm window. Therefore, it is best NOT to use spaces in filenames, use the underscore _ character instead, less problems all around.