The ligation dialog is a means for virtually ligating two (or more) DNA fragments. It can be invoked via Tools/Ligation or Ctrl-L.
The left list shows all potential DNA sequences to be ligated. Some of these are automatically selected, but selection can be manually changed. The right list shows the possible products of a ligation of the selected sequences. Some circular products will be shown in two forms (A-B and B-A), which only differ visually.
The selected products will be generated as new sequences on clicking the Ligate button.