From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 12:31:44 +0000 (+0100)
Subject: JAL-1684 use Muscle protein alignment as guide for cDNA alignment reconstruction.
X-Git-Tag: Release_2_10_0~456
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=3c1bd9d0ddf49f842ce1f19a11303b8e1bb106be

JAL-1684 use Muscle protein alignment as guide for cDNA alignment reconstruction.
---

diff --git a/examples/applets.html b/examples/applets.html
index ff97475..9e00bd5 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -177,8 +177,8 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
    code="jalview.bin.JalviewLite" width="140" height="35"
    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 <param name="permissions" value="sandbox"/>
-<param name="file" value="estrogenReceptorCdna.fa"/>
-<param name="file2" value="estrogenReceptorProtein.fa"/>
+<param name="file2" value="estrogenReceptorCdna.fa"/>
+<param name="file" value="estrogenReceptorProtein.aln"/>
 <param name="enableSplitFrame" value="true"/>
 <param name="scaleProteinAsCdna" value="true"/>
 <param name="showFullId" value="false"/>
@@ -192,8 +192,10 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
 </applet>
 </td>
       <td valign="center">Displays a split window view of protein
-        and its related cDNA.<br />Data retrieved from Uniprot and ENA,
-        after Thornton, Need and Crews, <a
+        and its related cDNA.<br />Proteins were aligned with <a
+        href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
+        via the Jalvew Desktop).<br />Data retrieved from Uniprot and
+        ENA, after Thornton, Need and Crews, <a
         href="http://dx.doi.org/10.1126/science.1086185">Science 19
           September 2003: 301 (5640), 1714-1717</a>
       </td>