X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FArchaeopteryx.wiki;h=abd0375d27ff0a54f5dd2a421326eb34212370c2;hb=9d627b6d40d2f38258ffe2cdebd82a2e8c1b9ea6;hp=6faaeae82091f52531c5a4820de4fbd7f65f69a0;hpb=6934907122ee17b8d127a18235ede33d81736924;p=jalview.git

diff --git a/wiki/Archaeopteryx.wiki b/wiki/Archaeopteryx.wiki
index 6faaeae..abd0375 100644
--- a/wiki/Archaeopteryx.wiki
+++ b/wiki/Archaeopteryx.wiki
@@ -1,3 +1,5 @@
+#summary Archaeopteryx Documentation
+
 = Archaeopteryx Documentation =
 <wiki:toc max_depth="3" />
 
@@ -6,16 +8,28 @@
 Under development!
 
 Documentation, tutorial, and examples for visualization, analysis, and editing of phylogenetic trees with [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx].
+Some (older) documentation can also be found [http://aptxevo.wordpress.com/ here].
+
+For developers: Information on the underlying [http://www.phylosoft.org/forester/ forester] framework is available [forester here].
 
 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
 
+
  
 Copyright (C) 2012 Christian M Zmasek. All rights reserved.
 
-
+----
 
 = Frequently Asked Questions =
 
 == How to read and display vector or expression data ==
 
-Aptx can be used to display vector or expression data associated with tree nodes.  
\ No newline at end of file
+Aptx can be used to display vector or expression data associated with tree nodes:
+
+  # Ensure the configuration file contains this line: "show_vector_data:               display yes"
+  # Start Aptx and read in a tree ([http://forester.googlecode.com/files/apaf.xml example tree])
+  # Open "Tools" menu and select "read Vector/Expression Values" to read in a matrix (of, for example, expression values) ([http://forester.googlecode.com/files/apaf_expression.tab example expression values])
+
+It is also possible to store vector data in phyloXML formatted files ([http://forester.googlecode.com/files/apaf_with_vector_data.xml example]).
+
+----
\ No newline at end of file