X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Freferenceseq.html;h=7c0e3dc6073616707fbacef66c3d7faf34e46267;hb=fae86f8127622397f9df1e120c85546f1656a33b;hp=912be55fdd33d9899590f29ff1328704ec475c5a;hpb=18ec5585c00cf8f8833c30f4dae5c04bc9ecfc65;p=jalview.git

diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html
index 912be55..7c0e3dc 100644
--- a/help/html/calculations/referenceseq.html
+++ b/help/html/calculations/referenceseq.html
@@ -31,12 +31,11 @@
     organisms that are similar to a newly sequenced gene, or when
     searching for structurally similar sequences for use in homology
     modelling.</p>
-<p>
+  <p>
     <strong>What happens when a reference sequence is defined ?</strong>
   </p>
-  <p>
-    The reference sequence for an alignment is indicated by its ID being
-    shown in bold. In addition:</p>
+  <p>The reference sequence for an alignment is indicated by its ID
+    being shown in bold. In addition:</p>
   <ul>
     <li><strong>Reference sequence numbering</strong>. Instead of
       column numbers, the alignment ruler shows the reference sequence
@@ -59,10 +58,10 @@
     <li><strong>Defining a reference when importing
         annotation</strong><br />Jalview automatically assigns a reference
       sequence when importing analysis results, such as those returned
-      from <a href="../webServices/jnet.html">JPred4</a> . A reference
+      from <a href="../webServices/jnet.html">JPred</a> . A reference
       sequence can also be assigned via the <a
-      href="../features/annotationsFormat.html#refsandviews">SET_REF</a> command in
-      an alignment annotation file.</li>
+      href="../features/annotationsFormat.html#refsandviews">SET_REF</a>
+      command in an alignment annotation file.</li>
   </ul>
   <p>
     <em>Reference sequence based alignment visualisation was