To select a tree just click on one of the list entries. Each of them represents a different example tree. Clicking on one of the buttons < show whole tree > or < show restricted tree > you will get a viewer window showing either the whole tree or an abstraction of it if the tree contains more than 300 leaves.
In such a viewer window you can double-click on an inner node to expand/collapse the node. With the right mouse button you will get a context sensitive popup menu which presents a choice of possible actions to you. The menu will depend on whether you have clicked on an inner node, a leaf node or the background. The sensitive areas for the nodes are the rectangles which represent the inner nodes and the (invisible) rectangles which follow the line endpoints leading to each leaf or collapsed subtree.
In order to be able to add a list of own trees by clicking on the button < (re)load local trees > you have to add some lines to your private policy file .java.policy to grant the applet access to a local tree directory on your computer. See below for more information and an example policy file.
There is also a more detailed description of the TreeWiz applet.
Access to local resources:
Usually an applet is not allowed to access any local resources such as files on your hard disk. In order to be able to read or write data from the machine the applet runs on you have to grant explicit access. By setting up a .java.policy file in your home directory you can control the things an applet is allowed to do. The TreeWiz applet is able to show trees which reside on your computer under the following conditions:
In your home directory there has to be a directory called trees (which also can be a link to another location). Place your tree files which have to be in Newick file format in this directory
The applet has to be able to read the property user.home and has to have read access to the trees directory. You can use my personal policy file (Linux version / WindowsNT version) as a template if you want.
For a deeper insight into the use of a policy file see the policy tool page for
Solaris and Linux or
Windows.
Example trees
puzzle.phylip This is a small phylogenetic tree with 24 different organisms
homeo-domain-tree.phylipThis is a tree which has been extracted from the SYSTERS tree. It contains all SwissProt proteins which own a homeodomain.
sigma-induced-tree.phylip This is a tree which has been extracted from the SYSTERS tree. It contains all SwissProt proteins which own a sigma-factor.
Newick file format:
The Newick tree file format (also named New Hampshire standard) describes trees (or forests to be correct) in a recursive way.
The format goes back to the early days of phylogeny and was informally developed during a meeting of the Society for the Study of Evolution (see also this page about the format located at CMBI)
As there seems to be no "official" specification for this format (at least I didn't find any) I specified my own grammar adding an optional type-tag to distinguish between trees with semantically different content. If you want to compare it to some other specification, just have a look at my grammar file.
Local copy of applet
If you want to use this applet locally you can download it from forest.jar. Just copy the jar-File and this html file to your server. Change the http address in the applet tag accordingly and, if you have put the jar file and the html file in different directories, also change the archive value in the applet tag. Create a subdirectory with the name tree in the codebase directory and put some example trees there.
The use of the applet is subject to the following copyright notice. If you use it, please include references to the EML and and to this copyright notice on your web page.