We notice bright green selections, taxonomic groups (internal node labels) that enclose their members - either showing them, or hiding them under a square outline. Each group has a bounding box, a name and some indication of the number of members within, as illustrated by this example,

The colon-separated numbers in parentheses are the numbers of selected nodes within and the total number, respectively. The scale bar is simply a visual representation of the same.

The horizontal bar that separates METHANOSARCINALES and METHANOSAETA will change position as you scroll the tree (under X the display updates continuously, under NT only when the scrollbar slider is released). Its purpose is to always show the hierarchy as a help to know where in the tree you are looking. As another assistant, the tree topology is always kept within the display, instead of vertical lines that run off the screen.

How To Leave

quit	Simply quits the applet without doing anything else.
<<<	Exits the applet but with a programmable action attached such as handing a set of selected organisms to some analysis. This is analogous to a word processor where the document is saved, as opposed to just quitting.

Colors and Fonts

Color	Here you can choose among a few preset display color combinations that each emphasize branches, labels, etc.
Font	Sets the display font to small, medium or large.

How to Collapse and Expand the Tree

The applet has three different collapse modes that help give the user better overview of large trees - we call it pruning, except the tree can be expanded to full size again after it has been 'pruned'.

NONE	This shows all terminal nodes (tips) and expands the tree to its fullest.
SOME	All named groups (internal nodes) within which no organisms have been selected (see below) are reduced to a square. The area of this square is proportional to the number of organisms hidden within.
MAX	This collapses the tree to show only selected nodes and their parents.

Different Modes and Their Actions

It is possible to both select, selectively collapse and edit labels - all by using the left mouse button. So for the applet to know which of these actions are intended, it has three modes that the user must change between: Select, Group and Label.

Select	After pressing this button, mouse clicks will select parts of the tree. Single labels may be selected by clicking on them, any subtree by clicking on the horizontal branch that leads to it, or a group by clicking on the small square at the upper left of its boundary box. To add to a previous selection, hold down the shift key in combination with the (left) mouse button. Using the shift key toggles previous selections, so this can also be used to de-select parts of a selection.
Group	To hide a set of nodes, click on the upper left of the box that encloses them. Click again to show the nodes again, this is a toggle. A click within the group square always expands. Tip: if your tree has no internal node labels, you may create one - see the following.
Label	In label mode, clicks will cause this small window to appear, in which you may enter, edit or delete the label. If you enter a label name where there was none, then a group box will be drawn when you press the OK button. Similarly, if you edit an existing label, then the group name will appear with the changed text. And if you delete an existing label, then the group box will disappear.

Slides or Transparencies

Do a screen dump: on Unix machines, the xv package does this well. There must be similar utilities on other systems. Then annotate the image further with Adobe Photoshop or Gimp, or similar, and print it to a PostScript printer.