Information
This program was created to aid anyone who has wanted to reproduce a tree from an image
or paper where access to the tree file or original data isn't available or there isn't
time to recompile it. This applet lets you copy the visual style of the tree manually in
a format that's easier to use than the usual mess of parenthesis or code that's required.
This applet has no way of taking into account confidence values or branch length - it allows
you to copy topology only. It is not intended for rigorous scientific work, simply for those
who would like to be able to investigate and perhaps rearrange a tree, or add colours/styling.
Information
It is recommended that you print off the tree you'd like to replicate, if possible, so you
can write on it. Then label the branch points however you like - simple numbers or letter
will work best.
Here I've labeled the branch points 'a' and 'b':
Now, simply define each branch point by stating what it contains.
Notice that if you are putting a lower-down branch point inside of a higher-up branch
point (here clade 'a' is nested in clade 'b'), the fact that 'a' is a branch-point name
is signified by putting an asterick (*) in front of it. This tells the program that 'a'
isn't a leaf, but contains further branches/leaves. Also notice that order is noted -
defining 'b' as '*a, rat' states that 'cat' and 'dog' branch above rat. Obviously the tree
is still the same, but keeping the order the same as the tree you are replicating can make
it easier to double-check that you have correctly copied the tree. (Note that some programs
you open the tree in may disregard this order.)
It is *very important* to not use a branch point until you have define
what it contains! In this example, it means not defining 'b' before you have defined 'a':
If you do this, your tree will be incorrect, with missing branches and leaves. To prevent
this, it is best to work from the deepest level of the tree outward.
There are two good ways of doing this with more complex trees:
A - Start from the top of the tree, and label branch points inwards until you
come to a branch point that includes branch points not yet defined - go out to these
and work inwards again.
B - Divide the tree into branching 'levels' and label each level, starting at the leaves,
working inwards.
The applet will give you two types of code: phyloXML and Nexus (.nexus, .nex). Copy the
resulting text out of the applet and into notepad or wordpad, but ensure you save it as
type 'All Files' and with the extension '.xml' or '.nex' after the name.
I would recommend Archaeopteryx for
viewing your file, as it opens both types of file and allows you to save them in phyloXML,
NHX, Nexus, and New Hampshire (Newick) formats, as well as export graphic images as PDF, PNG,
GIF, BMP, and JPG. You can also use it to rearrange your tree. If you would like to add
colour/labels to your tree, I recommend FigTree.
To reorganize 'tanglegrams' or host-parasite relationship phylogenies, I would recommend
TreeMap(v1.0). It will allow
you to import two trees and then define relationships between them.
TreeMap2 is
available for Mac usrs only. TreeMap3
has an automatic 'detangling' function that can be useful, but is unfinished and a little tricky to
run.*
*To run in Windows, download the files from the TreeMap3 website
and unzip them somewhere. Download this .bat file and place it in the
TreeMap3.0b.app/Contents/Resources/Java folder. You can then double-click it to run.
If you're hesitant downloading the file from this site, create a new file called 'run.bat' in
the folder and put the following text in it (all on one line):
java -Xms256M -Xmx1024M -classpath "jar_0.jar;jar_1.jar;junit.jar;junit.jar;iText-2.1.5.jar;iText-rtf-2.1.5.jar;iText-rups-2.1.5.jar" treemap.TreeMap
Code never lies, comments sometimes do.