#summary Archaeopteryx Documentation

= Archaeopteryx Documentation =
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= Introduction =

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.

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= 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:

  # 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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