Drawtree

© Copyright 1990-2013 by The University of Washington. Written by Joseph Felsenstein and Jim McGill. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

Drawtree interactively plots an unrooted tree diagram, with many options including orientation of tree and branches, label sizes and angles, and margin sizes. Particularly if you can use your computer screen to preview the plot, you can very effectively adjust the details of the plotting to get just the kind of plot you want.

To understand the working of Drawtree you should first read the Tree Drawing Programs web page in this documentation.

Java Interface

All Phylip programs will get Java interfaces in the 4.0 release. But under some operating systems there are currently serious problems with Drawtree, so it has received its Java interface early as part of the 3.695 bug fix release. We do not anticipate changing this Java interface substantially in the 4.0 release, but don't be surprised if we do.

This new Java interface supersedes the old character-mode menu interface. PHYLIP also contains versions of Drawgram and Drawtree that have the character-mode menu interface. We have kept these available because PHYLIP is used in many places as part of pipelines driven by scripts. Since these scripts do not usually invoke the preview mode of Drawtree, we have disabled the previewing of tree plotting in Drawtree in this release. Previewing is available in the version of Drawtree that has the interactive Java interface.

The Java interface is different from the previous character-mode menu interface; it calls the C code of Drawgram, which is in a dynamic library. Thus, after the previewing is done, the code producing final plot file should make plots that are indistinguishable from those produced by previous versions of Drawgram.

Java Menu Interface

The Java Drawtree Interface is a modern GUI. It will run only on a machine that has a recent version of Oracle Java installed. This is not a serious limitation because Java is freeware that is universally available.

When you start the Drawtree Java interface it looks similar to the following, which has been edited to generate the plot which follows:

It has all the usual GUI functionality: input and output file selectors, drop down menu options, data entry boxes and toggles. "Preview" brings up a nearly WYSIWYG preview window that displays the Postscript plot created by the current settings:

Each time you select "Preview" another preview window is generated, so that multiple previews can be visible. This allows you to compare various display options. When the plot has been fine tuned, clicking "Create Plot File" writes the Postscript file that generated the last Preview to the plot file specified. Note that if there are multiple preview windows open, the most recent one is the one that shows how the tree in the final plot file will look, since it will be plotted using the most recent settings.

All the functionality in the Java GUI is the same as in the equivalent menu item in the character-mode menu interface. To ease the transition, we have kept the text in the Java GUI as close as possible to the description in the character-mode menu interface. So, for example, "L" in the old interface, which has the helper message "Angle of labels", maps to "Angle of labels" in the new interface. All the detailed explanations of each label are found below.

Command Line Interface

The Command Line Interface gives the user access to a huge collection of both display systems and output formats (some of them are historical curiosities at this point, but they still work so there is no reason to remove them). It can also be driven by scripting because it is a command line interface. But, as most users have little experience with command line systems, it is a bit daunting.

As with Drawgram, to run Drawtree you need a compiled copy of the program, a font file, and a tree file. The tree file has a default name of intree. The font file has a default name of "fontfile". If there is no file of that name, the program will ask you for the name of a font file (we provide ones that have the names font1 through font5). Once you decide on a favorite one of these, you could make a copy of it and call it fontfile, and it will then be used by default.

Once these choices have been made you will see the central menu of the program, which looks like this:

Unrooted tree plotting program version 3.695 Here are the settings: 0 Screen type (IBM PC, ANSI)? ANSI P Final plotting device: Postscript printer B Use branch lengths: (no branch lengths available) L Angle of labels: branch points to Middle of label R Rotation of tree: 90.0 I Iterate to improve tree: Equal-Daylight algorithm D Try to avoid label overlap? No S Scale of branch length: Automatically rescaled C Relative character height: 0.3333 F Font: Times-Roman M Horizontal margins: 1.65 cm M Vertical margins: 2.16 cm # Page size submenu: one page per tree Y to accept these or type the letter for one to change

These are the settings that control the appearance of the tree, which has already been read in. You can either accept these as is, in which case you would answer Y to the question and press the Return or Enter key, or you can answer N if you want to change one, or simply type the character corresponding to the one you want to change (if you answer N it will just immediately ask you for that number anyway).

For a first run in the Java interface version you might accept these default values and see what the result looks like.

You can resize the preview window, though you may have to ask the system to redraw the preview to see it at the new window size.

Once you are finished looking at the preview, you will want to specify whether the program should make the final plot or change some of the settings. The possible settings are listed below.

When you are ready to produce the final plot file, you should use the button "Create Plot File" (if you are using the Java interface) or you should type Y (if you are using the character-mode menu). In the Java-interface version, the name of the plot file has been set in the dialog box near the top of the Java window. It defaults to plotfile.ps. In the character-mode menu, the file name defaults to plotfile.

If there is already a file of that name, the program will ask you whether you want to Overwrite the file, Append to the file, or Quit (in the character-mode menu version it also gives the option of writing to a new file whose name you will be asked to supply.

THE OPTIONS

Below I will describe the options one by one; you may prefer to skip reading this unless you are puzzled about one of them.

Postscript Font

(In the character-mode menu version, selection F). Allows you to select the name of the font that you will use for the species names. For each of the plot file formats, this will either choose the Postscript font (if they allow Postscript fonts) or the built-in Hershey font that most closely matches it. Please understand that for plot file formats that lack Postscript font support, you will get one of our five Hershey fonts. The plot file types that allow Postscript fonts are (as far as we know): Postscript, FIG 2.0, and Idraw. In the preview of the tree in the Java-interface version, actual Postscript fonts are always used, but with any plot file type other then these three, the font is replaced by the closest Hershey font. The size of the characters in the species names is scaled according to the character heights you have selected in the menu, whether plotter fonts or the Hershey font are used. Note that for some plotter drivers (in particular FIG 2.0 and PICT) Postscript fonts can be used in the final plot file only if the species labels are horizontal or vertical (at angles of 0 degrees or 90 degrees). Otherwise Hershey fonts will be used.

Use branch lengths

(In the character-mode menu version, selection B). Whether the tree has Branch lengths that are being used in the diagram. If the tree that was read in had a full set of branch lengths, it will be assumed as a default that you want to use them in the diagram, but you can specify that they are not to be used. If the tree does not have a full set of branch lengths then this will be indicated, and if you try to use branch lengths the program will refuse to allow you to do so. Note that there is no way to use negative branch lengths, so Drawtree automatically takes their absolute values, and thus will plot a branch that has length -0.1 as if it has length 0.1.

Angle of labels

(In the character-mode menu version, selection L). The angle of the Labels. Initially the branches connected to the tips will point to the middles of the labels. If you want to change the way the labels are drawn, the program will offer you a choice between Middle, Fixed, Radial, and Along as the ways the angles of the labels are to be determined. If you choose Fixed, you will be asked if you want labels to be at some fixed angle. This can be between 90.0 and -90.0 degrees and you can specify that. You may have to try different angles to find one that keeps the labels from colliding: I have not guarded against this. However there are additional options. Middle has the branch connected to that tip point to the midpoint of the label. It puts the label at a fixed angle of 0. Radial indicates that the labels are all aligned so as to point toward the root node of the tree. Along aligns them to have the same angle as the branch connected to that tip. This is particularly likely to keep the labels from colliding, but it may give a misleading impression that the final branch is long.

Angle of tree

(In the character-mode menu version, selection R). The rotation of the tree. This is initially 90.0 degrees. The angle is read out counterclockwise from the right side of the tree, so that increasing this angle will rotate the tree counterclockwise, and decreasing it will rotate it clockwise. The meaning of this angle is explained further under option A. As you rotate the tree, the appearance (and size) may change, but the labels will not rotate if they are drawn at a Fixed angle.

Arc of tree

(In the character-mode menu version, selection A). The Angle through which the tree is plotted. This is by default 360.0 degrees. The tree is in the shape of an old-fashioned hand fan. The tree fans out from its root node, each of the subtrees being allocated part of this angle, a part proportional to how many tips the subtree contains. If the rotation of the tree is (say) 90.0 degrees (the default under option R), the fan starts at +270 degrees and runs clockwise around to -90 degrees (i.e., it starts at the bottom of the plot and runs clockwise around until it returns to the bottom). Thus the center of the fan runs from the root upwards (which is why we say it is rotated to 90.0 degrees). By changing option R we can change the direction of the fan, and by changing option A we can change the width of the fan without changing its center line. If you want the tree to fan out in a semicircle, a value of a bit greater than 180 degrees would be appropriate, as the tree will not completely fill the fan. Note that using either of the iterative improvement methods mentioned below is impossible if the angle is not 360 degrees.

Iterate to improve tree

(In the character-mode menu version, selection I). Whether the tree angles will be Iteratively improved. There are three methods available:

no (Equal Arc)

This method, invented by Christopher Meacham in PLOTREE, the predecessor to this program, starts from the root of the tree and allocates arcs of angle to each subtree proportional to the number of tips in it. This continues as one moves out to other nodes of the tree and subdivides the angle allocated to them into angles for each of that node's dependent subtrees. This method is fast, and never results in lines of the tree crossing. However, it may result in rather large empty areas between subtrees. It is the method used to make a starting tree all three methods, so that the selection "no" leaves us with this tree and does not improve the tree beyond this.

Equal-Daylight algorithm

This is the default method. It iteratively improves an initial tree by successively going to each interior node, looking at the subtrees (often there are 3 of them) visible from there, and swinging them so that the arcs of "daylight" visible between them are equal. This is not as fast as Equal Arc but should never result in lines crossing. It gives particularly good-looking trees, and it is the default method for this program. It will be described in a future paper by me. This method has also been adopted by David Swofford in his program PAUP*.

n-Body algorithm

This assumes that there are electrical charges located along all the branches, and that they repel each other with a force that varies (as electrical repulsion would) as the inverse square of the distance between them. The tree adjusts its shape until the forces balance. This can be computationally slow, and can result in lines crossing. I find the trees inferior to the Equal-Daylight algorithm, but it is often worth a try.

Maximum Iterations

(Not available in the character-mode menu version). This is for the Equal-Daylight algorithm or the n-Body algorithm. It sets how many passes through the tree will be made when trying to achieve a good placement. The more the greater the accuracy of the solution will be, but the slower the program will run.

Regularize the angles

(in the character-mode menu version, selection G). If iterative improvement is not turned on in option I (so that we are employing the Equal Arc method), this option appears in the menu. It controls whether the angles of lines will be "regularized". Regularization is off by default. It takes the angles of the branches coming out from each node, and changes them so that they are "rounded off". This process (which I will not fully describe) will make the lines vertical if they are close to vertical, horizontal if they are close to horizontal, 45 degrees if they are close to that, and so on. It will lead to a tree in which angles look very regular. The size of angle to which they will round off the angles varies with the number of tips on the tree. You may or may not want that. If you are unhappy with the appearance of the tree when using this option, you could try rotating the angle of the tree slightly, as that may cause some branches to change their angle by a large amount, by having the angles be "rounded off" to a different value.

Try to aboid label overlap

(In the character-mode menu version, selection D). Whether the program tries to avoiD overlap of the labels. We have left this off by default, because it is a rather feeble option that is frequently unsuccessful, and often make the trees look weird. Nevertheless it may be worth a try.

Branch lengths

(In the character-mode menu version, selection S). On what Scale the branch lengths will be translated into distances on the output device. Note that when branch lengths have not been provided, there are implicit branch lengths of 1.0 per branch. This option will toggle back and forth between automatic adjustment of branch lengths so that the diagram will just fit into the margins, and you specifying how many centimeters there will be per unit branch length. This is included so that you can plot different trees to a common scale, showing which ones have longer or shorter branches than others. Note that if you choose too large a value for centimeters per unit branch length, the tree will be so big it will overrun the plotting area and may cause failure of the diagram to display properly. Too small a value will cause the tree to be a nearly invisible dot.

Relative character height

(In the character-mode menu version, selection C). The Character height, measured as a fraction of a quantity which is the horizontal space available for the tree, divided by one less than the number of tips. You need not worry about exactly what this is: you can always change the value (which is initially 0.3333) to make the labels larger or smaller. On output devices where line thicknesses can be varied, the thickness of the tree lines will automatically be adjusted to be proportional to the character height, which is an additional reason you may want to change character height.

Scale of branch length

(In the character-mode menu version, selection R). How the branch lengths will be recalculated into distances on the output device. Note that when branch lengths have not been provided, there are implicit branch lengths specified by the type of tree being drawn. In the Java interface version, you can enter how many centimeters there will be per unit branch length. In the character-mode version the selection will toggle back and forth between letting you select the scale and automatically rescaling the tree so that the diagram will just fit into the margins. This is included so that you can plot different trees to a common scale, showing which ones have longer or shorter branches than others. Note that if you choose too large a value for centimeters per unit branch length, the tree will be so big it will overrun the plotting area and may cause failure of the diagram to display properly. Too small a value will cause the tree to be a nearly invisible dot.

Margins:

(In the character-mode menu version, selection M). The horizontal and vertical margins in centimeters. You can enter new margins (you enter new values for both horizontal and vertical margins, though these need not be different from the old values). For the moment I do not allow you to specify left and right margins separately, or top and bottom margins separately. In a future release I hope to do so.

Final plot file type

(in the character-mode menu version, menu selection P). This allows you to choose the Plotting device or file format. We have discussed the possible choices in the draw programs documentation web page. In the Java version they are Postscript, PICT, PCL, Windows BMP, FIG 2.0, Idraw, VRML, or PCX. In the character-mode menu version there is a longer list of plot file types.

#

(charater-mode menu version only) The number of pages per tree. Defaults to one, but if you need a physically large tree you may want to choose a larger number. For example, to make a big tree for a poster, choose a larger number of pages horizontally and vertically (the program will ask you for these numbers), get out your scissors and paste or tape, and go to work.

O

(character-mode menu version only) This is an option that allows you to change the menu window to emulate an ANSI terminal or an IBM PC terminal. Generally you will not want to change this.

I recommend that you try all of these options (particularly if you can preview the trees). It is of particular use to try trees with different iteration methods (option I) and with regularization (option G). You will find that a variety of effects can be achieved.

I would appreciate suggestions for improvements in Drawtree, but please be aware that the source code is already very large and I may not be able to implement all suggestions.