To display the complement (3’ to 5’) of a sequence (displayed 5’ to 3’), check the Complement box in the Display tab. Note that the complement option is for display purposes only, you cannot select or edit the complement sequence. If you wish to create a separate document to work with the complement (not reverse complement) of a sequence, you will need to install the Complement or Reverse plugin by going to Tools → Plugins. Once the plugin is installed, go to Sequence → Complement only to create a new document containing the complement.
To reverse complement a nucleotide sequence (i.e. reverse the sequence direction and replace each base by its complement), click the R.C button above the sequence viewer, or go to Reverse Complement under the Sequence menu. You can also access this option right-clicking in the sequence viewer and selecting it from the popup menu. When you click Save after reverse complementing, the tag (reversed) will be added to the sequence name.
When only part of a sequence is selected, you can choose to either reverse-complement only the selected region and extract it to a new sequence document, or reverse complement the entire sequence. On alignment or contig documents you can reverse complement individual sequences within the alignment or assembly by selecting that sequence, and choosing reverse complement selected sequence.