Help (Main Page)

Welcome to the TreeGraph 2 help system

This MediaWiki provides the online help for the tree editor TreeGraph 2. You can access it from the help menu of the application or the context specific help buttons in all dialogs as well as directly with your browser. Additionally you can use the search field on the left to look for answers to your questions.

Video tutorials    Alphabetical index of articles    Available features (article about the TreeGraph 2 main menu)    Help by category    Visualizing node/branch data    TreeGraph 2 publication

Feature overview The application Main menu Tool bar Document window Synchronizing tree selections Import/export Open files (Newick, Nexus (including hot comment annotations), NeXML, PhyloXML) Adding support values (Merging support values from different analyses) Importing node/branch data (Importing annotations from tables) Importing ancestral state probabilities Exporting commands for ancestral state analyses Exporting trees as graphics Exporting trees as Newick/Nexus files Exporting node/branch data (Exporting annotations to tables) Exporting pie chart label colors Parts of a TreeGraph 2 document Document element Node Branch Label Text label Icon label Pie chart label Legend Scale bar Formatting Element formats Document formats Set colors by node/branch data (Allows you to display annotations as colors.) Set distance values by node/branch data (Allows you to display annotations e.g. as branch widths or text heights.) Scaling distance values Automatically position labels Annotations Node/branch data Text label Hidden node/branch data Adding support values Copying node/branch data Calculating node/branch data (Allows you to calculate annotations by mathematical expressions from other annotations.) Deleting node/branch data outside interval Data table of the document window Tree editing Inserting nodes Collapsing nodes Collapsing nodes by support Anchoring legends Copying/cutting document elements Ladderizing Sorting terminal nodes Moving nodes Rerooting Editing text element values Changing branch lengths Replace text in node/branch data

Questions? If you have further questions you could not find an answer to here: Ask a question on TreeGraph's ResearchGate project page Send us an e-mail to support@bioinfweb.info Citation TreeGraph 2 has been published in BMC Bioinformatics: Stöver BC, Müller KF: TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 2010, 11:7 The paper describes the features of TreeGraph 2 until version 2.0.40 and can be helpful to get an overview. Video tutorials In addition to the articles on single features a set of screencasts is provided that allow you to learn how to use TreeGraph 2 step by step. Currently the following screencasts are available: Combining support values from different analyses in one tree Creating trees by hand (e.g. helpful in teaching) Displaying taxon counts of the angiosperm orders as branch widths Additional tutorials can be found at the tutorial main page. Contributing to this wiki This wiki can currently only be edited by registered users. Anyway everybody who wants to contribute to this help system is welcome. If you want to be a registered user or have any comments or requests feel free to send an e-mail to support bioinfweb.info Help for developers If you are a developer and want to use TreeGraph 2 in one of your projects you should have a look at the development section which contains a documentation of the design concept as well as complete Javadocs. If you want to call TreeGraph 2 by command line from your application or script you can have a look at the Command line options article. Note that you can only integrate TreeGraph 2 into your software under the terms of the GNU General Public License.