Edited wiki page RIO through web user interface.

[jalview.git] / wiki / Archaeopteryx.wiki

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+#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.  
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+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]).
+
+----
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