X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2FArchaeopteryx.wiki;h=abd0375d27ff0a54f5dd2a421326eb34212370c2;hb=9d627b6d40d2f38258ffe2cdebd82a2e8c1b9ea6;hp=d0ceae001b88129c75dce17a785ad0b467faf567;hpb=38e0f5b001a56b339f9a6476ae1f2a40b3c06ca4;p=jalview.git diff --git a/wiki/Archaeopteryx.wiki b/wiki/Archaeopteryx.wiki index d0ceae0..abd0375 100644 --- a/wiki/Archaeopteryx.wiki +++ b/wiki/Archaeopteryx.wiki @@ -1,3 +1,5 @@ +#summary Archaeopteryx Documentation + = Archaeopteryx Documentation = @@ -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]. -Information on the underlying forester framework is here: [forester]. +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]) \ No newline at end of file +---- \ No newline at end of file