1 #summary Archaeopteryx Documentation
3 = Archaeopteryx Documentation =
4 <wiki:toc max_depth="3" />
10 Documentation, tutorial, and examples for visualization, analysis, and editing of phylogenetic trees with [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx].
11 Some (older) documentation can also be found [http://aptxevo.wordpress.com/ here].
13 For developers: Information on the underlying [http://www.phylosoft.org/forester/ forester] framework is available [forester here].
15 Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
19 Copyright (C) 2012 Christian M Zmasek. All rights reserved.
23 = Frequently Asked Questions =
25 == How to read and display vector or expression data ==
27 Aptx can be used to display vector or expression data associated with tree nodes:
29 # Ensure the configuration file contains this line: "show_vector_data: display yes"
30 # Start Aptx and read in a tree ([http://forester.googlecode.com/files/apaf.xml example tree])
31 # 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])
33 It is also possible to store vector data in phyloXML formatted files ([http://forester.googlecode.com/files/apaf_with_vector_data.xml example]).