+#summary Archaeopteryx Documentation
+
= Archaeopteryx Documentation =
<wiki:toc max_depth="3" />
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