To select a tool click on the icon corresponding to the tool you want to use. Once you have selected a tool the cursor will change to the appropriate shape. To manipulate the tree click the cursor on a branch; the corresponding operation will be performed on that branch (unless the desired operation is invalid, in which case the tree editor gently "beeps" and ignores the command). The default tool is the arrow tool, which is used for moving branches.
Move branch
A branch can be picked up and moved to another part of the tree by clicking on the branch and dragging it to the new position. The branch being moved will be highlighted with a different colour, and the cursor will change from an arrow to a small diamond:
Drag the diamond cursor to the position you want to move the branch, and release the mouse button. If the new placement is invalid (for example, moving a branch onto one of its descendants) the tree editor will gently "beep" and ignore your request.
Collapse branch
Clicking with this tool on an internal branch deletes that branch produces a polytomy. The editor ignores attempts to delete terminal branches.
Collapse clade
Clicking with this tool on an internal branch collapses the clade above that branch
Reroot
Clicking on a branch with this tool reroots the tree on that branch.
The next four tools change the appearance of the tree in the window, but do not affect the cladistic topology. They cannot be undone.
Rotate branches
This tool rotates the descendants of a binary node, so that the left descendant is now the right descendant, and visa-versa. You can only use this tool on binary internal nodes. If you want to rearrange the descendants of a polytomy you must use the next tool.
Exchange branches
To rearrange the order of the descendants of a polytomy use this tool to interchange pairs of branches. Click on one descendant, drag the cursor onto the other descendant, and release the mouse button.
Ladderize left
This tool orders the subtree rooted at the branch clicked on so that the "heavier" nodes (those nodes with the largest clusters) appear leftmost (uppermost on the screen).
Ladderize right
This tool orders the subtree rooted at the branch clicked on so that the "heavier" nodes (those nodes with the largest clusters) appear rightmost (lowermost on the screen).
The tree editor remembers the previous tree, so that you can undo a change and recover the old tree by choosing Undo from the Edit menu, or by using these keys:
Z (MacOS)
Ctrl + Z (Windows)
Choosing the Undo command again restores the tree you just undid. Undo is only available for the operations that materially affect the tree topology: move branch, collapse branch, collapse clade, and reroot. Cosmetic changes (such as rotate branches) cannot be undone.
The Undo menu item will reflect which type of move can be undone; for example the menu item will read "Undo move branch" if you are using the move branch tool.