X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FArchaeopteryx.wiki;h=99c65889935acdab556f98b81b53b014f57c2b2a;hb=2c743e8da2d45c8dec1694a3edddd3797b64fb4d;hp=811d8d5e68d3b40f09eff3933c28157c1fbb99ba;hpb=45779141e3fa54cf6766ea41d8481f509c54aac0;p=jalview.git diff --git a/wiki/Archaeopteryx.wiki b/wiki/Archaeopteryx.wiki index 811d8d5..99c6588 100644 --- a/wiki/Archaeopteryx.wiki +++ b/wiki/Archaeopteryx.wiki @@ -1,3 +1,5 @@ +#summary Archaeopteryx Documentation + = Archaeopteryx Documentation = @@ -5,14 +7,18 @@ Under development! -Documentation, tutorial, and examples for visualization, analysis, and editing of phylogenetic trees with [http://www.phylosoft.org/archaeopteryx/ Archaeopteryx]. +Documentation, tutorial, and examples for visualization, analysis, and editing of phylogenetic trees with [https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/ Archaeopteryx]. +Some (older) documentation can also be found [http://aptxevo.wordpress.com/ here]. + +For developers: Information on the underlying [https://sites.google.com/site/cmzmasek/home/software/forester/ forester] framework is available [forester here]. + +Author: [https://sites.google.com/site/cmzmasek/ Christian Zmasek], Sanford-Burnham Medical Research Institute -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 = @@ -20,9 +26,10 @@ Copyright (C) 2012 Christian M Zmasek. All rights reserved. Aptx can be used to display vector or expression data associated with tree nodes: - 1 Ensure the configuration file contains this line: "show_vector_data: display yes" - - 2 Start Aptx and read in a tree ([http://forester.googlecode.com/files/apaf.xml example tree]) + # 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]) - 3 Open "Tools" menu and select "read Vector/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