Copy/paste the Phylip treefile to the input window
Click on "Build Tree from Input" to build the listbox
tree display
Select a new root node in the listbox
Output the subtree rooted at the selected node
Copy/paste the output window to a new treefile
Drag the mouse in the graph window to zoom in (or out if you hold
down shift)
Click in the graph window to restore zoom to
normal
Notes:
New: you can now save your graph as a
Macintosh PICT (version 2) file so you can edit and print it using other
programs. This can be done via the Virtual Clipboard or directly
to your machine, depending on whether you've installed this
program there. If you copy your tree as a PICT file to the
virtual clipboard, you can retrieve it and save it on your machine
by going to "View Virtual Clipboard" (see below).
The number in the first column of the listbox is the depth of the node.
This is followed by its name, number of children, and number of descendent
leaves.
Double clicking on a node in the list box opens
or closes its subtree. The first checkbox determines whether this operates
on all of the node's descendents, or on just its children.
The number of "descendents" refers to the number of leaf nodes
in the subtree rooted at a node; i.e. interior nodes are not counted.
By default, the output tree will include the entire subtree rooted at
the node selected in the listbox, regardless of how much of the subtree
is open in the listbox. If you want to shrink subtrees into single nodes
in the output tree, close them in the listbox and uncheck the second checkbox
below. Interior nodes representing shrunken subtrees are given names of
the form xxx" in the output.
Thanks to Greg Wilson for the sample data from bison.
Browse this tree, or click on "Clear Inputs" to use your
own data.
(Visit Cluster, a clustering program
that produces output this program can use.)
Note on Pages
Some browsers limit the size of text windows, so this program allows
for bigger input and output using multiple pages. Each page is limited
to around 10000 characters. To see if you have filled a page, try typing
more characters at the end of the window. When you copy/paste in and out
of this program, you have to do so one page at a time; the program has
no control over cut/paste, and so can't tell when your input is bigger
than one page.
The Virtual Clipboard lets you paste data into or copy data out of multi-page windows.
The ---> VC and <--- VC buttons move data to and from the virtual clipboard.
If you see a "Browse" button below, then your browser will also let you
copy a file on your machine to the Virtual Clipboard. You can then paste it from the V.C. into the
calculator's input windows.
Name of file:
The Virtual
Clipboard is Brainless
Is your window full of garbage after pasting? Unfortunately, the Virtual
Clipboard knows nothing about file formats, so cutting and pasting directly
from an Excel file will fill your window with junk (ie. raw Excel file
bytes). You can, however, copy from the open Excel worksheet to a text
editor, then save as text in a new file which you can then copy to the
Virtual Clipboard. You can also just save a copy of your Excel file in
tab-delimited text format, and copy that file to the VC. The point of the
VC is just to help work around the limitations on window size in Netscape,
MS Explorer, and probably other browsers.
Installing TreeToy on Your Machine
If your connection to this server is slow, you can get your own copy of the program:
use your browser's File | Save as... feature to save
this HTML/php file to a directory on your machine - save it as TreeToy.html
To run the program, use your browser to open your copy of TreeToy.html
(For older browsers, you might have to unzip the archive TreeToy.zip in this directory.
Be sure to preserve the directory structure stored in the archive.)
Credits
This applet was inspired by DRAWTREE, from the Phylip
package by Joel Felsenstein et al. My thanks to them for making it free.
Thanks for motivation and feedback to Greg Wilson, Curtis Strobeck,
and David Paetkau.
This Java and HTML web page is by John
Brzustowski. I appreciate any comments or criticisms. Although I try
to ensure the correctness of these programs, you use them entirely
at your own risk. There is no warranty!