PhylodendronPhylodendron
Phylodendron is an application for drawing phylogenetic trees, used in evolutionary
biology. It will read tree data in New Hampshire (Newick) format, then display
graphical views of the phylogenetic tree. Various options allow you to modify,
adorn and edit the tree. Standard application functions to save, print, edit and
manage preferences are included. This program will not estimate nor produce the
tree data. For that, software such as Phylip, Clustal W, and others may be used.
Phylodendron is available at
Phylodendron is written as a Java application. This means that it will run on most personal computers and workstations as a standard program. This application is an enhancement of the Mac Hypercard program "Tree Draw Deck" released by the author in 1990.
One problem in using this program is that Java is still in preliminary stages. You
currently must fetch and install a Java runtime system to use it. This can be obtained
freely on the Internet. See for example
<http://www.javasoft.com/nav/download/index.html>
Developers will find the source code in the iubio:/molbio/java/source folders. These
files are not needed for running the program. Phylodendron is built on the
beginnings of an application framework for Java, which may make it easier to
develop new applications.
Phylodendron is available over the Internet at
Macintosh users will find these files in the archive file phylodendron.hqx. MSWindows users will find program files in the archive file phylodendron.zip. Unix and others will find just the program files in the archive file phylodendron.tar.gz. You likely will need to fetch (see below) and install the Java runtime for your system. Newer operating systems (MacOS 8, Warp, Solaris 2.6) include java runtime systems; though you may want to update them to current versions.
As I've learned with other multi-platform applications that I make available to the
bioscience community, there are difficulties involved in the time it takes me to
update multiple archives for different computer systesm. The simplest way for me
to distribute and update this software is to provide it as separate files, e.g., the
pictures and documents and p-code files, and to update each one individually as
needed. For example, I update this document after I've already produced some of the
archive files. So I will also provide the most current version of this software in its
un-archived form. You may find the most current versions by looking in the all
systems/ folder. Within that, the folder called local/ has those items specific to each
computer system. With a bit more programming effort, I hope to have the
application do some of its own updating as needed (see below Updates).
This current release is based on the Java Developer Kit 1.0.2. To run it, you should
have installed the runtime compatible with JKD1.0.2. This can be found through
Javasoft, and at various mirror sites around the world.
http://www.javasoft.com/products/jdk/1.0.2/index.html
For Java runtimes for various operating systems, see
http://www.javasoft.com/products/jdk/jdk-ports.html
A newer Java version, 1.1, became available in 1997. I will provide an update to this program with this new Java version, perhaps by the start of 1998. For now, Java version 1.0.2/1.0.3 runtimes are needed to run the application.
1. Keep in the same folder whereever you prefer, the application Phylodendron, the TreeApp.jcode Java class archive, and the data folder.
2. Use the MRJ installer from Apple Computer to install this Java runtime software. If you have MacOS 8, this is included as part of the OS. However, at the first release of MacOS 8, the MRJ included is an early, slower version. You should upgrade to the MRJ 1.5 release.
3. Put the contents of "->System/Extensions" into System Folder:Extensions:
4.Install the Internet Config application, if you don't have it. MacOS 8 includes this program. This free, widely used program enables links among Internet aware applications. This application uses it to call others like Netscape to open network links and the help document.
1. Keep in the same folder whereever you prefer, the program batch file TREEAPP.BAT, the Phylodendron.jcode Java class archive, and the data folder.
2. Install a Java Runtime system for MS Windows. Install it in a standard location,
which will be entered in the TREEAPP.BAT file. A recommended Java runtime is
found at http://www.javasoft.com/products/jdk/1.0.2/installation-win32-x86.html
You may want to install this in the same folder as you store SeqPup (and other java
applications). Or you may want to install this in a general MSWindows folder,
perhaps C:\WINDOWS\JAVA. I don't know of a prefered location yet on MS
Window systems for Java runtime files. You will need to edit the batch file (step 3)
to account for this location.
3. Edit the TREEAPP.BAT file to make the path names match the file locations on
your computer.
set base=\temp\java
set appclass=%BASE%\treeapp\TreeApp.jcode
set java=%BASE%\javaThe distribution zip archive containes application files in the path \TEMP\JAVA\treeapp\ and Java runtime files in the path \TEMP\JAVA\java\. If you unzip it with those names preserved, then you shoud be able to run the program from the batch file TREEAPP.BAT.
For the application to link properly to Netscape or other Internet browser, you may
need to edit the preferences file. You can do this from within the application; see the
Options/Edit Framework ... Menu. Or you can edit the file dclap.ini which will be
created in the \java\ folder. In either case, you want to enter the variable name
user.openurl= then the full path to your browser to be sure that it works properly.
This path may well be the same on your system as mine, which is as follows. Note the
quote marks (due to space in name) and the double backslashes \\ which are required
to insert one \.
user.openurl="C:\\Program Files\\Netscape\\Navigator\\Program\\netscape.exe"
If you use the Edit prefs menu, after editing close the window. You should be
prompted to save changes; do so.
For Sun Solaris computers (SPARC and Intel):
http://www.javasoft.com/products/jdk/1.0.2/installation-solaris2.html
For IBM Warp on Intel, IBM AIX, and MS Windows 3.1 computers:
http://www.ibm.com/Java/tools/jdk.html
http://ncc.hursley.ibm.com/javainfo/hurindex.html
For DEC Digital Unix computers:
http://www.unix.digital.com/products/internet/jdk102_main.html
For various Linux on Intel systems:
http://www.blackdown.org/java-linux.html
For Silicon Graphics IRIX computers:
SGI has hidden their Java runtime version 1.0.2. Sorry.
contact SGI for more details at http://www.sgi.com/
Whatever runtime system you install, it must be called with the TreeApp.jcode file. See
the file treeapp which is a small shell script to do this on Unix. Edit that to suit your
system needs.
You need to define the user.openurl= variable to find your Netscape or equivalent. You can do this from within the application; see the Options/Edit basic prefs... Menu. Or edit the file ~/.dclaprc directly to enter such a line. The variable line for my unix system is
user.openurl=/usr/local/bin/netscape
Also, you might instead use a shell script (like the "netscape.sh" included). If you rename that to netscape, edit it to suit, and put in the folder with TreeApp.jcode file, it may take the place of editing the preference file.
Currently Java 1.0.3 does not understand printing (a slight oversight due to the Xwindow history of Java). The current Print command just sends postscript of a drawing to the user.print file.
Joe Felsenstein has provided for many years the excellent phylogenetic analysis package PHYLIP that most of you are likely familiar with. While most of the applications in this package don't require any fancy user-interface, the drawing programs DRAWTREE and DRAWGRAM were, to my mind, just begging for a better user interface for Macintosh users to see and print trees. In 1990, I took Joe's code and stuffed it into a Mac Hypercard application within a few weekends, producing Tree Draw Deck.
This Hypercard version proved useful to people, but wasn't a complete drawing application. It had shortcomings in saving and editing files. An attempt of mine to overcome this a few years later wasn't successful. With enough time..., but I was fighting Hypercard's limitations then.
One of the very nice features of Hypercard is that one can put easy-to-use faces onto programs quickly. Since the decline of Hypercard and Macintoshes, I've missed this form of rapid application development, and haven't yet found an equivalent. With some more work, I hope that Java can take its place. Those of you who have seen Tree Draw Deck should note similarities with the "About Phylodendron" window.
I do have high hopes now for Java as an Internet Hypercard. Phylodendron, and its companion test app LoopDloop [java], gave me a feeling that Java is ready for complex application development, and it has the potential for rapid application development with a good app framework. The two programs I have now in it are both small, MacDraw style scientific drawing apps. They share about 60 - 70% of their code. Improvements in one will lead to improvements in the other in many cases, and that also will hold for future applications written to this framework. I hope to provide at least one application for the FlyBase drosophila database and at some point a version of the sequence analysis application SeqPup in this Java framework.
This framework,dubiously named DCLAP, was started with the NCBI toolkit, a cross
platform C toolkit on which Entrez, Sequin and other apps from NCBI are written (thank
you Jonathan Kans and colleages at NCBI for this wonderful, free toolkit). On top of this
toolkit I wrote a C++ framework which is meant to handle much of the basic application
chores such as document opening, saving, doc and window management, menu and
command management, etc. With the advent of Java as a C++-like language that has
broad support and funding of tools from the commercial sector, but which also is available in
free form at its basics, it looked like a good underpining for rapid, cross-platform app
development. However, neither NCBI toolkit nor Java nor other sources provide the kind of
application framework freely that makes it quick and easy to produce robust, easy to use,
full featured applications for the biosciences. As I write new applications, I aim at
improving such a framework so that the next application can be written more quickly than
the last. The source code for this framework, in C++ and now its beginnings in Java, is
available freely to others for scientific application development. The current Java version
of DCLAP is preliminary, and will change significantly when converted to JDK version 1.1,
and has a ways to go for being a good app framework. However I find it now very helpful in
producing new applications, and hope that other programmers may also find it useful.
Developers will find the source code for this application and others in the
iubio:/molbio/java/source folders.
Searching for a name for an application is always a chore for programmers. A memorable
name and cute icons are de rigueur for successful software these days; functionality can be
secondary. I didn't want another variation on treedraw, drawtree, treetool, etc.
Phylodendron just struck me as a natural for this sort of software. The cute icon was
modelled by a pretty Philodendron plant here. The working name has been TreeApp; you
will find that name used some places (e.g., the TreeApp.zip file).
Both of these options, and the help command, link through an accessory program for opening URLs (Internet universal resource locators). Typically this accessory will be Netscape or the like software. In order to use this accessory program properly, it must be configured on your computer.
For Macintosh users, this involves installing Internet Config, a small free program used
by many other Internet applications. Internet Config must be installed on your system,
and you need to configure it to specify Helpers for at least the following protocols: ftp, file,
http, mailto.
These helpers may all be Netscape.
For Unix users, this involves setting the preference called "user.openurl" to the proper path to reach Netscape or other Internet applications. See also the small shell script that can be used to customize this function.
For MsWindows users, this also involves setting the preference called "user.openurl" to the proper path to reach Netscape or other Internet applications.
the primary selection tool, for selecting tree, nodes, and other objects. Also for
moving objects.
shift a node within a tree. This tool lets you change node positions at the same
branching level. This changes the overall format of the tree without affecting the
meaning of the dendrogram. When you select this tool, use the mouse to select a
node first, then drag that node toward other nodes. While you drag, a rectangle will
hilight to show which other nodes are at the same level and capable of interchange
with the selected node. Node shifting for unrooted trees uses a smaller highlit box
than for rooted. For rooted trees, you may use a shift-key plus this tool to have the
smaller highlit box and avoid some node conflicts.
resize an object. Use the mouse cursor after selecting this tool to frame the rectangle which will contain the tree. The tree will be drawn to fit that rectangle.
Tree diagram -- draws an unrooted tree diagram.
Cladogram -- nodes are connected to other nodes and to tips by
straight lines going directly from one to the other. This gives a V-shaped appearance.
Phenogram -- nodes are connected to other nodes and to other tips by
a horizontal and then a vertical line. This gives a particularly precise idea of horizontal
levels.
Curvogram -- nodes are connected to other nodes and to tips by a
curve which is one fourth of an ellipse, starting out horizontally and then curving upwards to
become vertical. This pattern was suggested by Joan Rudd.
Eurogram -- so-called because it is a version of cladogram diagram
popular in Europe (name courtesy of David Maddison). Nodes are connected to other nodes
and to tips by a diagonal line that goes outward and goes at most one-third of the way up to
the next node, then turns sharply straight upwards and is vertical. Unfortunately it is
nearly impossible to guarantee, when branch lengths are used, that the angles of divergence
of lines are the same.
Swoopogram -- this option (suggested by James Archie), connects two
nodes or a node and a tip using two curves that are actually each one-quarter of an ellipse.
The first part starts out vertical and then bends over to become horizontal. The second
part, which is at least two-thirds of the total, starts out horizontal and then bends up to
become vertical. The effect is that two lineages split apart gradually, then more rapidly,
then both turn upwards.
Regular - will make an unrooted tree have regular angles. This 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.
Use node lengths - if a tree has branch lengths, these may be use to specify the length of each node, or not.
Intermediate places a node halfway between its immediate descendants.
Weighted places it closer to that descendant who is closer vertically as well.
Centered centers the node below the horizontal positions of the tips that are descended
from that node.
V-shaped is designed to yield a v-shaped tree of regular appearance,, if there are no branch
lengths being used. With branch lengths it will not necessarily do so.
Innermost chooses a center for the tree, and always places interior nodes below the innermost of their immediate descendants. This leads to a tree that has vertical lines in the center, like a tree with a trunk.
Adornments -
Circle - append a circle to the node.
Box - append a box to the node.
Hide - make invisible the node, and all descendant nodes.
Fill symbol - fill the circle or box
No label - don't draw a label for this node.
Future releases may offer more node adornment symbols.
Font style - choose the font, font size, font face, and color for selected nodes. Currently the color also is applied to branch lines and adornments as well as font [future releases may separate this].
Show node comments - display any comment field associated with a node. Comments are entered in a tree file in [brackets].
Number inner nodes - put a number beside each inner node.
The New Hampshire Standard for representing trees in computer-readable form makes use of the correspondence between trees and nested parentheses, noticed in 1857 by the famous English mathematician Arthur Cayley. If we have this rooted tree:
A D
\ E /
\ C / /
\ ! / /
\ ! / /
B \ ! / /
\ o /
\ ! /
\ ! /
\ ! /
\ ! /
\! /
o
!
!
(B,(A,C,E),D);
The tree ends with a semicolon. Everything after the semicolon in the input file is ignored, including any other trees. The bottommost node in the tree is an interior node, not a tip. Interior nodes are represented by a pair of matched parentheses. Between them are representations of the nodes that are immediately descended from that node, separated by commas. In the above tree, the immediate descendants are B, another interior node, and D. The other interior node is represented by a pair of parentheses, enclosing representations of its immediate descendants, A, C, and E.
Tips are represented by their names. A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. In the programs a maximum of 30 characters are allowed for names: this limit can easily be increased by recompiling the program and changing the CONSTant declaration for "nch" at the beginning of the program. Trees can have 300 nodes (including tips), this is controlled by the CONSTant "maxnodes" and can also be changed.
Because you may want to include a blank in a name, it is assumed that an underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in. Any name may also be empty: a tree like
(,(,,),);
is allowed. Trees can be multifurcating at any level (while in many of the programs multifurcations of user-defined trees are not allowed or restricted to a trifurcation at the bottommost level, these programs do make any such restriction).
Branch lengths can be incorporated into a tree by putting a real number, with or without
decimal point, after a node and preceded by a comma. This represents the length of the
branch immediately below that node. Thus the above tree might have lengths represented
as:
(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);
These programs will be able to make use of this information only if lengths exist for every branch, except the one at the bottom of the tree.
The tree starts on the first line of the file, and can continue to subsequent lines. It is best to proceed to a new line, if at all, immediately after a comma. Blanks can be inserted at any point except in the middle of a species name or a branch length.
The above description is of a subset of the New Hampshire Standard. For example, interior nodes can have names in that standard, but if any are included the present programs will omit them.
To help you understand this tree representation, here are some trees in the above form:
((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700,
seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201,
weasel:18.87953):2.09460):3.87382,dog:25.46154);
(Bovine:0.69395,(Gibbon:0.36079,(Orang:0.33636,(Gorilla:0.17147,(Chimp:0.19268,
Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);
(Bovine:0.69395,(Hylobates:0.36079,(Pongo:0.33636,(G._Gorilla:0.17147,
(P._paniscus:0.19268,H._sapiens:0.11927):0.08386):0.06124):0.15057):0.54939,
Rodent:1.21460);
();
((A,B),(C,D));
(Alpha,Beta,Gamma,Delta,,Epsilon,,,);
The New Hampshire Standard was adopted June 26, 1986 by an informal committee meeting during the Society for the Study of Evolution meetings in Durham, New Hampshire and consisting of James Archie, William H.E. Day, Wayne Maddison, Christopher Meacham, F. James Rohlf, David Swofford, and myself.
DRAWTREE and DRAWGRAM are interactive tree-plotting programs that take a tree
description and read it. DRAWTREE plots unrooted trees and DRAWGRAM plots rooted
cladograms and phenograms. These programs are descended from PLOTGRAM and
PLOTREE written by Christopher Meacham. I have incorporated his code for fonts and his
plotter drivers, and in DRAWTREE have used some of his code for drawing unrooted trees.
In both programs I have also included some plotter driver code by David Swofford, Julian
Humphries and George D.F. "Buz" Wilson, to all of whom I am very grateful. Mostly,
however, they consist of my own code.