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TreeSnatcher: A Phylogenetic Tree Capturing Tool
Introduction:
TreeSnatcher is a GUI-driven Java application for the semi-automatic recognition
of multifurcating phylogenetic trees in pixel images. The program accepts an
image file as input and analyzes the topology and the metrics of a tree depicted
with user assistance. The analysis is carried out in a multiple-stage process
using basic algorithms from the field of image analysis. It yields a Newick
expression that represents the tree structure optionally including branch lengths.
TreeSnatcher can process trees with more than 100 leaves or more in a few seconds.
Availability:
Mac OS X Tiger
Please feel free to download the program version for your operating system available
now. The manual does not contain a description of the Graphical User Interface.
You are therefore kindly encouraged to also download the accompanying PDF tutorial
to get a picture of what TreeSnatcher can do, cannot do, and how you can use it.
Linux, Windows
Due to differences in the inner workings between the Apple JAVA implementation
and the Sun JAVA implementation for Linux/Windows we could not provide these
versions in July as promised. We apologize for the inconvenience.
These versions are now available.
Important Hints:
Some of you have thankworthy addressed the question to us in which cases TreeSnatcher
might output a wrong Newick expression:
The skeletonization algorithm used in TreeSnatcher to thin out the foreground is
currently not entirely intelligent. This means that the program might erroneously
claim nodes in the tree even if the user has provided an image that is perfectly
suitable. If these wrong nodes are not deleted, the Newick expression
will be wrong. This is an incident that will be solved in future versions of
TreeSnatcher.
To avoid frustration please carefully read the section "Where TreeSnatcher finds
nodes" in the accompanying PDF. Remember that up to now TreeSnatcher measures
branch lengths "from node to node" (we are already working on this topic).
Please understand that this program is a work-in-progress.
We will be very grateful for bug reports and welcome your suggestions.
Reference:
The program is described in the following article:
Thomas Laubach and Arndt von Haeseler (2007)
TreeSnatcher: Coding Trees from Images. Bioinformatics, to be published
If you are using TreeSnatcher, please cite this article.
Download:
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