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[jalview.git] / wiki / Archaeopteryx.wiki

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@@ -1,3 +1,5 @@
+#summary Archaeopteryx Documentation
+
 = Archaeopteryx Documentation =
 <wiki:toc max_depth="3" />
 
@@ -6,8 +8,9 @@
 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 forester framework is available [forester 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
 
@@ -15,7 +18,7 @@ Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical R
  
 Copyright (C) 2012 Christian M Zmasek. All rights reserved.
 
-
+----
 
 = Frequently Asked Questions =
 
@@ -25,6 +28,8 @@ 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" ([http://forester.googlecode.com/files/apaf_expression.tab example expression values])
+  # 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]).
 
-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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