java -jar PathToYourFolder/TreeGraph.jar. Windows users can alternatively start "TreeGraph.exe".)
Future version will also contain installers for Windows and Linux platforms which will also be able to register different file types (e.g. *.xtg or *.tre) to be opened with TreeGraph 2.
Since there are currently no installers available for TreeGraph 2 you would have to associate file types like Newick, Nexus or the native format of TreeGraph 2 (XTG) manually if you e.g. want to be able to open these files with TreeGraph 2 by a double click. On windows platforms we recommend to associate files with TreeGraph.exe instead of TreeGraph.jar.
Furthermore you can use the file icons which are contained in the installation directory of TreeGraph 2 in the icons subfolder.