Hypergeny

Welcome to Hypergeny. Hypergeny is an online tool for viewing large phylogenetic trees. We hope to help researchers visualise and understand large phylogenetic trees by offering a hyperbolic tree browser.

Quick View From File: From Url: From Copy/Paste: Input is a valid newick file. No tree to upload? View Tree. Need help with java installation?

Currently available:

• Quick view: Visualize your own trees.
• Sample Trees: example trees from published papers.
• API: Integrate our viewer in your own web applications. Beta: please do not integrate this in a production environment as the specifications will change.
• Standalone version: Download here

Browser Requirements

Using a relatively recent browser with javascript support is encouraged: Netscape / Mozilla 6+, Internet Explorer 5+.

Java v1.4.1+ required. Get it here: Windows/Linux/Solaris - OSX. You only need the JRE. SDK is not required to run the applets on this site. You may need to contact your system administrator if you don't have admin rights on your workstation.

Test your configuration here. The java application should start automatically in about 30 seconds. If it doesn't you'll probably have to install a newer java version. Use the links above to find and install the right java version for your machine.

Linux: Don't forget to link your plugin to your browser, e.g. ln -s /usr/java/j2re1.4.2_02/plugin/i386/ns610-gcc32/libjavaplugin_oji.so /usr/lib/mozilla/plugins

Sample Trees

Van de Peer, Y., Rensing, S.A., Maier, U.-G. & De Wachter, R. (1996) Substitution rate calibration of small ribosomal subunit RNA identifies chlorarachniophyte nucleomorphs as remnants of green algae. Proc. Natl. Acad. Sci. USA 93, 7732-7736. View Tree

API

The hyperbolic tree viewer can be integrated in existing web applications by sending a well-formed HTTP-POST request to http://bioinformatics.psb.ugent.be/hypergeny/api/. The tree to be displayed should be in standard Newick format and can either be included in the POST request or loaded from an existing url.

Below are the settings required to view your own tree by HTTP-POST request:

1. Building the request
• enctype : "MULTIPART/FORM-DATA"
• method : "POST"
• action : " http://bioinformatics.psb.ugent.be/hypergeny/api/ "
2. Arguments to pass in the request
• tree_url: url to online Newick file.
• tree_payload: content of a Newick file as text-string, no newlines or special characters please

Copy/paste example forms below.

Load from url		Load from file content
<FORM ENCTYPE="MULTIPART/FORM-DATA" METHOD="POST" ACTION="http://bioinformatics.psb.ugent.be/hypergeny/api/" TARGET="new_window"> <INPUT TYPE="HIDDEN" NAME="tree_url" VALUE="http://bioinformatics.psb.ugent.be/hypergeny/sample_trees/tree_from_paper_1.nh"> <INPUT TYPE="HIDDEN" NAME="upload_option" VALUE="tree_url"> <INPUT TYPE="SUBMIT" VALUE="View Tree" LABEL="View Tree"> </FORM>	or	<FORM ENCTYPE="MULTIPART/FORM-DATA" METHOD="POST" ACTION="http://bioinformatics.psb.ugent.be/hypergeny/api/" TARGET="new_window"> <INPUT TYPE="HIDDEN" NAME="tree_payload" VALUE="(A,B,C,(D,E));"> <INPUT TYPE="HIDDEN" NAME="upload_option" VALUE="tree_payload"> <INPUT TYPE="SUBMIT" VALUE="View Tree" LABEL="View Tree"> </FORM>