Reference Sequence Alignment Views

The reference sequence for an alignment is indicated by its ID being shown in bold. When a reference sequence has been defined, the Format→Show unconserved option highlights mutations with respect to the reference sequence, rather than the alignment's consensus sequence.

• Jalview automatically assigns a reference sequence when JPred4 predictions are imported.
• Assigning a reference sequence
  A sequence can be marked as the reference sequence by right-clicking on it's ID to open the popup menu, and selecting the "(Sequence ID)→Mark as Reference" entry."

Reference sequence based alignment visualisation was introduced in Jalview 2.9.