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+
+
+
+Reference Sequences
+
+
+
+ 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.
+
+