- <li><strong>Pad Gaps<br>\r
- </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
+ <li><strong>Pad Gaps<br>\r
+ </strong><em>When selected, the alignment will be kept at minimal\r
+ width (so there no empty columns before or after the first or last aligned\r
+ residue) and all sequences will be padded with gap characters to\r
+ the before and after their terminating residues.<br>\r
+ This switch is useful when making a tree using unaligned\r
+ sequences and when working with alignment analysis programs which\r
+ require 'properly 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
+ </em></li>\r