TreeSnatcher Plus: A Phylogenetic Tree Capturing Tool
TreeSnatcher Plus is a GUI-driven Java application that automates the generation of a machine- readable representation of multifurcating phylogenetic trees contained in pixel images. It uses image processing methods to prepare the image and to detect the tree structure. The user supervises the semi-automatic recognition process and makes corrections to the image and to the topology where necessary. At the end the program produces a Newick tree code that represents the tree structure optionally including branch lengths.
TreeSnatcher Plus is an extended and re-conceptualized version of TreeSnatcher. It is well fitted to support the research on complex phylogenies and will be helpful if one wants to combine phylogenies based on a collection of already published trees that are not electronically available. Moreover, TreeSnatcher Plus is also suited for educational purposes as it allows the user to construct their own trees and to modify existing topologies.
Mac OS X
The program version from 2010 was developed on an Intel MacBook with MacOSX 10.4 and 2GB RAM.
The program version from 2010 was tested with 32bit Windows XP and Windows 7.
This is the new main development platform for TreeSnatcher Plus. The Linux and Windows executables from June 2012 represent the newest program version.
I cannot check whether it also runs on MacOSX and Windows.
My machine is an IBM compatible PC running Ubuntu Linux 10.11 with Java 1.6.0_29 64bit.
The universal source code for all versions is available below.
There are currently no new individual executables for MacOSX.
If the Linux executable does not work on your machine, please run TreeSnatcher Plus from its source code.
You need at least a JDK 1.6 (Java Development Kit) from Oracle in order to compile the sources.
If you wish to try the experimental tip label recognition option (OCR) (Linux and Windows), please run TreeSnatcher Plus from its source code.
Please consult the section 'USING THE SOURCE CODE' in tsReadme.txt' (below).
Your help is appreciated
This program is under constant development. We will be very grateful for bug reports and welcome your suggestions.
We thank Yannick Schrader-Schilkowsky for proofreading and suggestions.
The Windows and the Linux versions use the packages gOCR by Joerg Schulenburg (jocr.sourceforge.net) which was published under the GPL.
The Windows version uses the program pngtopnm from the package pngUtils (http://gnuwin32.sourceforge.net/packages/pngutils.htm).
TreeSnatcher Plus Poster (A TreeSnatcher Plus conference poster: Thomas Laubach and Martin J. Lercher)
TreeSnatcher Plus is described in the following article:
Thomas Laubach, Arndt von Haeseler and Martin J. Lercher (2012), TreeSnatcher Plus: Capturing Phylogenetic Trees from Images. BMC Bioinformatics 2012, 13:110; DOI: 10.1186/1471-2105-13-110
TreeSnatcher, the ancestor of this program, is described in the following article:
Thomas Laubach and Arndt von Haeseler (2007), TreeSnatcher: Coding Trees from Images. Bioinformatics 2007 23(24):3384-3385; DOI: 10.1093/bioinformatics/btm438
Part of this work was supported by the Wiener Wissenschafts-, Forschungs- und Technologiefonds awarded to Arndt von Haeseler (CIBIV, Vienna) (Website of the Center for Integrative Bioinformatics Vienna)
We tested the performance of TreeSnatcher Plus on the 100 benchmark trees for TreeRipper provided by Joseph Hughes and on additional files found via a Google search using the keyword 'phylogeny'.
Please feel free to download the TreeSnatcher Snapshot files below.
You are kindly encouraged to also download the accompanying PDF tutorials which serve as a manual for TreeSnatcher Plus.
Alternatively they are accessible from within the application itself. Sadly, this does not work on all operating systems.
You need a PDF viewer for your operating system.
The tutorials are here
tsImpression_MacOSX.png (A screenshot of TreeSnatcher Plus running on Mac OS X)
tsImpression_Windows.png (A screenshot of TreeSnatcher Plus running on Windows XP)
tsImpression_Linux.png (A screenshot of TreeSnatcher Plus running on Ubuntu Linux)
tsReadme.txt (The ReadMe for TreeSnatcher Plus from June 2012)
TreeSnatcherPlus for Intel Mac OS X.zip (TreeSnatcher Plus - Intel Mac OS X Executable, updated June 24 2010)
TreeSnatcherPlus for Windows.zip (TreeSnatcher Plus - Windows Executable, updated June 24 2010)
TSP_June2012_Windows.zip (TreeSnatcher Plus - Windows Executable, updated June 2012)
TreeSnatcherPlus for Linux.zip (TreeSnatcher Plus - Linux Executable, updated June 24 2010)
TSP_June2012_Linux.jar (TreeSnatcher Plus - Linux Executable, updated June 2012)
TSP_Sources_Dec11.zip (TreeSnatcher Plus - Source code, updated December 2011)
TSP_Sources_Feb12.zip (TreeSnatcher Plus - Source code, updated February 2012)
tspBenchmarks1.zip (TreeSnatcher Plus Snapshots for benchmarking, part 1)
tspBenchmarks2.zip (TreeSnatcher Plus Snapshots for benchmarking, part 2)
tspBenchmarks3.zip (TreeSnatcher Plus Snapshots for benchmarking, part 3)
tspBenchmarks4.zip (TreeSnatcher Plus Snapshots for benchmarking, part 4)
tspBenchmarks5.zip (TreeSnatcher Plus Snapshots for benchmarking, part 5)
TreeSnatcher Plus is a non-profit project. It is published under the GNU General Public License.
Mail contact: Thomas Laubach