2. Data File of Trees
Please refer to sample tree files (NHF.TRE and ODEN.TRE) for the data formats. Because they are text files, you can change the tree-shape and OTU names by editing them by word processors. In Newick Standard (New Hampshire Format) tree files, the outermost parentheses have either two (rooted trees) or three (unrooted trees) elements. DendroMaker can read both types of tree files. Please crick here for Newick Standard (New Hampshire Format). DendroMaker is also applicable to ODEN format tree files, as before. Please crick here for Oden format tree files. The length of OTU names should not be more than 255 characters. There is no limitation to the number of OTUs.

3. Editing the Tree
All commands can be chosen from the menu. Keyboard shortcuts are assigned to almost all commands. You do not need to press the Command key to use key commands. The list of commands will be shown if HELP is selected from the apple menu. Below is the list of commands for DM4.1.

'Reform' menu
 T : Move the root to the midpoint of the path between two most distant 
     OTUs.
(upper or lower arrows) : Move the root on the upper (or lower) branch 
     of the upper (or lower) node of the current root.
 D : Display or remove the branch at the root.
 G : Change the proportion of two branches at the root.
 E : Exchange the branches at a node indicated.
123: Automatic exchange of branches.
 M : Display or remove the names of OTUs.  Either names or numbers can 
     be shown.
 N : Display or remove the OTU numbers.
 B : Display or remove the lengths of branches.
 J : Display the scale bar.  Multiple bars of different lengths can be 
     shown.
 K : Remove the scale bar.
 +-: Let the lines of branches thicker (+) or thinner (-).
 F : Change the width of margins of the window.
 L : Change the interval between two OTUs.

'File' menu
 O : Input a new tree file and draw a tree.
 W : Close a tree window.
 S : Save a (modified) tree file in the ODEN format.
 Revert: Revert the tree before editing.
 Save As NHF: Save the tree file into the Newick (Rooted) or Newick 
              (Unrooted) formats.
 Sava As PICT : Save the tree as a PICT file.
 P : Print the tree.
 Q : Quit the program.

4. How to Determine the 'root' Position
To change the root position of the trees displayed, you need to use ^v (arrows) and E commands. After determining a position of a new root, you need to move the position step by step, finally to the position you desired. Furthermore, the proportion of two branches derived from the root can be changed by 'G' command. Thus, it is possible to move the root to any point of the tree. Although this operation may be a little bit difficult for the first time, anyone will be accustomed to it.
Unrooted trees such as NJ do not actually have roots. To draw unrooted trees in a rooted form, you have to prepare an outgroup which is apparently distant from other OTUs. The 'T' command of this program searches for the longest path between all pairs of OTUs, and put the root on the midpoint of the path. Thus, the 'T' command does not necessarily find the correct root.

5. How to Print
The tree shown on the screen can be saved in PICT file by selecting 'Save As PICT' command. The PICT files are readable and modifyable by most graphics software. It is also possible to print directly from DendroMaker to printers. A command to save into PostScript files has been removed in version 4 (it will be resumed if requested).

6. Known Problems
Below is a known problem of this program. Be careful, although I think this is not a very serious problem in practice. This point will be improved in future. Pleaes notify the author if you find another problems.

(1) The program sometimes terminates when trying to open a damaged tree file.