3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Reference Sequences</title>
27 <strong>Reference Sequence Alignment Views</strong>
30 The reference sequence for an alignment is indicated by its ID being
31 shown in bold. When a reference sequence has been defined, the <strong>Format→Show
32 unconserved</strong> option highlights mutations with respect to the
33 reference sequence, rather than the alignment's consensus sequence.
37 <li>Jalview automatically assigns a reference sequence when <a
38 href="../webServices/jnet.html"
39 >JPred4</a> predictions are imported.
41 <li><strong>Assigning a reference sequence</strong><br /> A
42 sequence can be marked as the reference sequence by right-clicking
43 on it's ID to open the popup menu, and selecting the "<strong>(Sequence
44 ID)→Mark as Reference</strong>" entry."</li>
47 <em>Reference sequence based alignment visualisation was
48 introduced in Jalview 2.9.</em>