- </strong><em>Adds gaps to the end of all the sequences so they are all \r
- the same length. This is useful for making a tree using unaligned sequences.<br>\r
- You may set the default gap character in <a href="../features/preferences.html">preferences</a>. \r
+ </strong><em>When selected, the alignment will be kept at minimal width \r
+ (so there no empty columns before or after the first or last aligned residue) \r
+ and all sequences will be padded with gap characters to the before and \r
+ after their terminating residues.<br>\r
+ This switch is useful when making a tree using unaligned sequences and \r
+ when working with alignment analysis programs which require 'properly \r
+ aligned sequences' to be all the same length.<br>\r
+ You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. \r