From: jprocter <Jim Procter>
Date: Mon, 15 Nov 2010 11:00:40 +0000 (+0000)
Subject: 2.6.1 update
X-Git-Tag: Release_2_7~378
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git

2.6.1 update
---

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index d416dfa..3e41ba3 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1"  ?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index 9af3f7d..6a22aef 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -1,6 +1,6 @@
 <html>
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
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  * 
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diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index bfae345..ab2310f 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -1,6 +1,6 @@
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  * 
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diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html
index 26a47b6..627dccf 100755
--- a/help/html/calculations/pairwise.html
+++ b/help/html/calculations/pairwise.html
@@ -1,6 +1,6 @@
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  * 
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diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index ce188bd..9ec1fe8 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,6 +1,6 @@
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  * 
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diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html
index 03c5b39..3350733 100755
--- a/help/html/calculations/quality.html
+++ b/help/html/calculations/quality.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/calculations/recoverInputdata.html b/help/html/calculations/recoverInputdata.html
index 1d36e29..6781e77 100644
--- a/help/html/calculations/recoverInputdata.html
+++ b/help/html/calculations/recoverInputdata.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html
index 7effbe5..4b8fe7b 100755
--- a/help/html/calculations/redundancy.html
+++ b/help/html/calculations/redundancy.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index 13c3ff9..29aaa12 100755
--- a/help/html/calculations/sorting.html
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diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 0e9ba3e..26a24c7 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index 67a92c4..32db2ce 100755
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index fb4e878..75ae927 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -1,6 +1,6 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
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diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 360ec41..3db00dd 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/blosum.html b/help/html/colourSchemes/blosum.html
index ec38cd8..5f4231e 100755
--- a/help/html/colourSchemes/blosum.html
+++ b/help/html/colourSchemes/blosum.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/buried.html b/help/html/colourSchemes/buried.html
index 176b7fe..2a91baf 100755
--- a/help/html/colourSchemes/buried.html
+++ b/help/html/colourSchemes/buried.html
@@ -1,6 +1,6 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
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diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html
index ecca772..0e57626 100755
--- a/help/html/colourSchemes/clustal.html
+++ b/help/html/colourSchemes/clustal.html
@@ -1,6 +1,6 @@
 <html>
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
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  * 
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diff --git a/help/html/colourSchemes/conservation.html b/help/html/colourSchemes/conservation.html
index 95d9f83..1affe45 100755
--- a/help/html/colourSchemes/conservation.html
+++ b/help/html/colourSchemes/conservation.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/helix.html b/help/html/colourSchemes/helix.html
index 111eac4..9013253 100755
--- a/help/html/colourSchemes/helix.html
+++ b/help/html/colourSchemes/helix.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/hydrophobic.html b/help/html/colourSchemes/hydrophobic.html
index 619bc4b..75ccc6f 100755
--- a/help/html/colourSchemes/hydrophobic.html
+++ b/help/html/colourSchemes/hydrophobic.html
@@ -1,6 +1,6 @@
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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
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diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html
index 7aecc23..79a6012 100755
--- a/help/html/colourSchemes/index.html
+++ b/help/html/colourSchemes/index.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/nucleotide.html b/help/html/colourSchemes/nucleotide.html
index 4735bc4..8e2aa8b 100755
--- a/help/html/colourSchemes/nucleotide.html
+++ b/help/html/colourSchemes/nucleotide.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/pid.html b/help/html/colourSchemes/pid.html
index 05b464c..c2a7b9f 100755
--- a/help/html/colourSchemes/pid.html
+++ b/help/html/colourSchemes/pid.html
@@ -1,6 +1,6 @@
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diff --git a/help/html/colourSchemes/strand.html b/help/html/colourSchemes/strand.html
index a5842d8..79704ba 100755
--- a/help/html/colourSchemes/strand.html
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diff --git a/help/html/colourSchemes/taylor.html b/help/html/colourSchemes/taylor.html
index 605e25b..9202c85 100755
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diff --git a/help/html/colourSchemes/textcolour.html b/help/html/colourSchemes/textcolour.html
index a56d8e6..dc2b5ec 100644
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diff --git a/help/html/colourSchemes/turn.html b/help/html/colourSchemes/turn.html
index 3bacbc9..98a25aa 100755
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diff --git a/help/html/colourSchemes/user.html b/help/html/colourSchemes/user.html
index 2fc26e3..9617bee 100755
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diff --git a/help/html/colourSchemes/zappo.html b/help/html/colourSchemes/zappo.html
index 0b27f85..743ccb2 100755
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diff --git a/help/html/editing/index.html b/help/html/editing/index.html
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diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
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index 9beaa7c..38d17e2 100755
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diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html
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diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index 5641d90..b322e20 100755
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  * 
  * This file is part of Jalview.
diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index 2b7a303..d9aa13f 100644
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html
index 015b5b1..046a326 100644
--- a/help/html/features/hiddenRegions.html
+++ b/help/html/features/hiddenRegions.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/jalarchive.html b/help/html/features/jalarchive.html
index c501ed9..c26393f 100755
--- a/help/html/features/jalarchive.html
+++ b/help/html/features/jalarchive.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index fb93bea..6aa2eaf 100644
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html
index 17b6fce..106cf4b 100644
--- a/help/html/features/multipleViews.html
+++ b/help/html/features/multipleViews.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/newkeystrokes.html b/help/html/features/newkeystrokes.html
index 69e175f..af2750c 100644
--- a/help/html/features/newkeystrokes.html
+++ b/help/html/features/newkeystrokes.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/overview.html b/help/html/features/overview.html
index 471b7be..a0aa3af 100755
--- a/help/html/features/overview.html
+++ b/help/html/features/overview.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html
index 67dbc43..5c81f40 100755
--- a/help/html/features/pdbviewer.html
+++ b/help/html/features/pdbviewer.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index cc45784..03b4993 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/search.html b/help/html/features/search.html
index 956ab12..8173f32 100755
--- a/help/html/features/search.html
+++ b/help/html/features/search.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index d9d51ae..d47a472 100755
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index a51aa95..c32d8fe 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html
index 808286c..0137634 100644
--- a/help/html/features/seqmappings.html
+++ b/help/html/features/seqmappings.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 71c2011..ad78549 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/features/wrap.html b/help/html/features/wrap.html
index 201ff06..bbb15bb 100755
--- a/help/html/features/wrap.html
+++ b/help/html/features/wrap.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/index.html b/help/html/index.html
index 676af1a..cedc202 100755
--- a/help/html/index.html
+++ b/help/html/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/export.html b/help/html/io/export.html
index 1860b4a..bd0f708 100755
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
index 95a6d71..f701dd0 100755
--- a/help/html/io/fileformats.html
+++ b/help/html/io/fileformats.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/index.html b/help/html/io/index.html
index cf7dbfb..0cadedc 100755
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/io/modellerpir.html b/help/html/io/modellerpir.html
index c5839ad..143d2e4 100755
--- a/help/html/io/modellerpir.html
+++ b/help/html/io/modellerpir.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html
index f821c23..70cab61 100755
--- a/help/html/jalviewjnlp.html
+++ b/help/html/jalviewjnlp.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -66,7 +66,7 @@
 		&lt;jar href="wsdl4j.jar"/&gt;
 		&lt;jar href="xercesImpl.jar"/&gt;
 		&lt;jar href="xml-apis.jar"/&gt;
-		&lt;property name="jalview.version" value="2.6"/&gt;
+		&lt;property name="jalview.version" value="2.6.1"/&gt;
   &lt;/resources&gt;
   &lt;application-desc main-class="jalview.bin.Jalview"/&gt;
 &lt;/jnlp&gt;
diff --git a/help/html/keys.html b/help/html/keys.html
index 3787710..4404da4 100755
--- a/help/html/keys.html
+++ b/help/html/keys.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/memory.html b/help/html/memory.html
index ed005bd..857c29a 100755
--- a/help/html/memory.html
+++ b/help/html/memory.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -47,7 +47,7 @@ The way you increase the memory settings for the JVM depends on which installati
       need to <a href="jalviewjnlp.html">make your own jnlp file</a> and add the following parameter into the
       &lt;resources&gt; element.
     <pre>
-&lt;j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/&gt;
+&lt;j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/&gt;
 </pre>
     Save the jnlp file somewhere and then - if you start Jalview through your
     web browser, point your browser at the file's url, othewise simply run javaws
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 06384f6..8156e93 100755
--- 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 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 89a8286..b604c89 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 451fb09..85ec95c 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html
index 7f4f317..10ec9c7 100755
--- a/help/html/menus/alwcolour.html
+++ b/help/html/menus/alwcolour.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html
index d010c6c..9710de1 100755
--- a/help/html/menus/alwedit.html
+++ b/help/html/menus/alwedit.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html
index c300cfb..fd2ebe5 100755
--- a/help/html/menus/alwfile.html
+++ b/help/html/menus/alwfile.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html
index 98a1abe..d7e8908 100644
--- a/help/html/menus/alwformat.html
+++ b/help/html/menus/alwformat.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwselect.html b/help/html/menus/alwselect.html
index b84733a..31809a2 100644
--- a/help/html/menus/alwselect.html
+++ b/help/html/menus/alwselect.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 46df611..75e3904 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index 5b06f55..e108ded 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/index.html b/help/html/menus/index.html
index f423b47..fa2b1a5 100755
--- a/help/html/menus/index.html
+++ b/help/html/menus/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 61063ed..4f66696 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 8c85b93..bac5a96 100755
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/misc/aaproperties.html b/help/html/misc/aaproperties.html
index 09e0e0a..2a4266a 100755
--- a/help/html/misc/aaproperties.html
+++ b/help/html/misc/aaproperties.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/misc/aminoAcids.html b/help/html/misc/aminoAcids.html
index 3a4cdf1..7b7e6c4 100755
--- a/help/html/misc/aminoAcids.html
+++ b/help/html/misc/aminoAcids.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/misc/geneticCode.html b/help/html/misc/geneticCode.html
index 07922cf..967b0ed 100755
--- a/help/html/misc/geneticCode.html
+++ b/help/html/misc/geneticCode.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/privacy.html b/help/html/privacy.html
index 01ad39c..f46b528 100644
--- a/help/html/privacy.html
+++ b/help/html/privacy.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html
index 013e0ca..e91d114 100644
--- a/help/html/vamsas/index.html
+++ b/help/html/vamsas/index.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html
index e54d5dd..867299a 100644
--- a/help/html/webServices/JABAWS.html
+++ b/help/html/webServices/JABAWS.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/clustalw.html b/help/html/webServices/clustalw.html
index 120a186..81ccc4e 100755
--- a/help/html/webServices/clustalw.html
+++ b/help/html/webServices/clustalw.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html
index 23d6991..1a03352 100644
--- a/help/html/webServices/dbreffetcher.html
+++ b/help/html/webServices/dbreffetcher.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index a12d7b3..939db64 100755
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -1,6 +1,6 @@
 
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html
index 3537554..79320f0 100755
--- a/help/html/webServices/jnet.html
+++ b/help/html/webServices/jnet.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/mafft.html b/help/html/webServices/mafft.html
index d3dd142..052e565 100644
--- a/help/html/webServices/mafft.html
+++ b/help/html/webServices/mafft.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
index a203849..0d413fc 100644
--- a/help/html/webServices/msaclient.html
+++ b/help/html/webServices/msaclient.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/muscle.html b/help/html/webServices/muscle.html
index 04fe696..1a3de9f 100755
--- a/help/html/webServices/muscle.html
+++ b/help/html/webServices/muscle.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html
index 649cc67..842cc90 100644
--- a/help/html/webServices/urllinks.html
+++ b/help/html/webServices/urllinks.html
@@ -1,6 +1,6 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/webServicesParams.html b/help/html/webServices/webServicesParams.html
index 714dd5c..3bec481 100644
--- a/help/html/webServices/webServicesParams.html
+++ b/help/html/webServices/webServicesParams.html
@@ -1,6 +1,6 @@
 
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
diff --git a/help/html/webServices/webServicesPrefs.html b/help/html/webServices/webServicesPrefs.html
index a581761..2d5d3ee 100644
--- a/help/html/webServices/webServicesPrefs.html
+++ b/help/html/webServices/webServicesPrefs.html
@@ -1,6 +1,6 @@
 
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
