git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JAL-1620 version bump and release notes
[jalview.git] / help / html / menus / alignmentMenu.html
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index f67faa9..966c005 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -62,18 +62,16 @@
                                                Select the format of the text by selecting one of the following
                                                menu items.</em>
                                        <ul>
-                                               <li><strong>FASTA</strong> <em></em>
-                                               </li>
-                                               <li><strong>MSF</strong>
-                                               </li>
-                                               <li><strong>CLUSTAL</strong>
-                                               </li>
-                                               <li><strong>BLC</strong>
-                                               </li>
-                                               <li><strong>PIR</strong>
-                                               </li>
-                                               <li><strong>PFAM</strong>
-                                               </li>
+                                               <li><strong>FASTA</strong> </li>
+                                               <li><strong>MSF</strong></li>
+                                               <li><strong>CLUSTAL</strong></li>
+                                               <li><strong>BLC</strong></li>
+                                               <li><strong>PIR</strong></li>
+                                               <li><strong>PFAM</strong></li>
+                                               <li><strong>PileUp</strong></li>
+                                               <li><strong>AMSA</strong></li>
+                                               <li><strong>STH</strong></li>
+                                               <li><strong>Phylip</strong></li>
                                        </ul></li>
                                <li><strong>Print (Control P)<br> </strong><em>Jalview
                                                will print the alignment using the current fonts and colours of
@@ -203,9 +201,9 @@
                                                the last redundancy deletion.</em>
                                </li>
                                <li><strong>Pad Gaps<br> </strong><em>When selected,
-                                               the alignment will be kept at minimal width (so there no empty
+                                               the alignment will be kept at minimal width (so there are no empty
                                                columns before or after the first or last aligned residue) and all
-                                               sequences will be padded with gap characters to the before and
+                                               sequences will be padded with gap characters before and
                                                after their terminating residues.<br> This switch is useful
                                                when making a tree using unaligned sequences and when working with
                                                alignment analysis programs which require 'properly aligned