TreeSnatcher Plus: A Phylogenetic Tree Capturing Tool
Please also check the TreeSnatcher Plus main page for updates.
Introduction
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 his own trees and to modify existing topologies.
Availability
Mac OS X
Please download and try out the Mac OS X version of TreeSnatcher Plus.
The main development platform is an Intel Apple Macintosh running Mac OS X 10.6.3 with the newest Java version.
The application has been thoroughly tested on this architecture.
Windows
Please download and try out the Windows version of TreeSnatcher Plus.
It has been tested with 32 bit Windows XP and Windows 7.
Due to a bug in the Java for Windows Native Look & Feel-implementation this version uses the cross-platform Look & Feel.
This version lacks a progress indicator.
Linux
Please download and try out the Linux version of TreeSnatcher Plus.
It has been tested with 32 bit Ubuntu Linux 10.4.
This version lacks a progress indicator and the quadratic curve drawing functionality. It uses the system mouse cursors.
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.
The (formatted) source code for all versions will be made available upon request.
Your help is appreciated
This program is under constant development.
We will be very grateful for bug reports and welcome your suggestions.
References
The ancestor of this program, TreeSnatcher, 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,
PMID: 17893085
Part of this work was supported by the Wiener Wissenschafts-, Forschungs-
und Technologiefonds awarded to Arndt von Haeseler
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(CIBIV, Vienna)
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Website of the Center for Integrative Bioinformatics Vienna
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Tutorials
You need a PDF viewer for your operating system.
TreeSnatcher Plus for Mac OS X uses Preview.app.
TreeSnatcher Plus for Linux uses Okular.
TreeSnatcher Plus for Windows uses the default PDF viewer.
The tutorials are here
Downloads
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tsReadme.txt
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The ReadMe for TreeSnatcher Plus from June 2010
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TreeSnatcher Plus is a non-profit project. It is published under the GNU General Public License.
Mail contact: Thomas Laubach, laubach{at}cs.uni-duesseldorf.de.
