JAL-2089 Merge branch releases/Release_2_10_Branch to master

[jalview.git] / help / html / na / index.html

diff --git a/help/html/na/index.html b/help/html/na/index.html
index 05454d8..17f2252 100644 (file)
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -57,17 +57,16 @@ td {
   way:
   <ul>
     <li><em>RFAM</em> - Sequences can be <a
-      href="../features/seqfetch.html"
-    >fetched</a> from the RFAM database by accession number or ID.</li>
+      href="../features/seqfetch.html">fetched</a> from the RFAM
+      database by accession number or ID.</li>
     <li><em>Stockholm files</em> - WUSS (or VIENNA) dot-bracket
       notation found in the secondary structure annotation line will be
       imported as sequence or alignment associated secondary structure
       annotation.</li>
     <li><em>Clustal files</em> - certain RNA alignment programs,
-      such as <a
-      href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
-    >LocaRNA</a> output consensus RNA secondary structure lines in the
-      line normally reserved for the Clustal consensus line in a clustal
+      such as <a href="http://rna.informatik.uni-freiburg.de/LocARNA">LocaRNA</a>
+      output consensus RNA secondary structure lines in the line
+      normally reserved for the Clustal consensus line in a clustal
       file.</li>
     <li><em>RNAML</em> Jalview can import RNAML files containing
       sequences and extended secondary structure annotation derived from
@@ -79,7 +78,7 @@ td {
     the alignment will have a secondary structure line shown below it,
     and a number of additional options become available:
   <ul>
-    <li><a href="../colourschemes/rnaHelicesColouring.html">RNA
+    <li><a href="../colourSchemes/rnahelicesColouring.html">RNA
         Helix colouring</a> - highlights columns of alignment involved in
       particular RNA helices, Uses the first displayed secondary
       structure annotation.</li>
@@ -103,9 +102,9 @@ td {
       per-sequence secondary structure is available).</li>
   </ul>
   <p>
-    <strong>Pseudo-knots</strong><br /> Jalview 2.8.2 introduced limited
-    support for working with structures including pseudoknots. Where
-    possible, extended WUSS symbols (e.g. different types of
+    <strong>Pseudo-knots</strong><br /> Jalview 2.8.2 introduced
+    limited support for working with structures including pseudoknots.
+    Where possible, extended WUSS symbols (e.g. different types of
     parentheses, or upper and lower case letters) are preserved when
     parsing RNA structure annotation and will be shaded differently when
     displayed in the structure.<br /> Extended WUSS annotation is also