TreeSnatcher Plus: A Phylogenetic Tree Capturing Tool

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 their own trees and to modify existing topologies.

Availability

Mac OS X

The program version from 2010 was developed on an Intel MacBook with MacOSX 10.4 and 2GB RAM.

Windows

The program version from 2010 was tested with 32bit Windows XP and Windows 7.

Linux

This is the new main development platform for TreeSnatcher Plus.
My machine is an IBM compatible PC running Ubuntu Linux 10.11 with Java 1.6.0_29 64bit.

Source Code

This is the newest program version. The unified source code for all versions is available below.
There are currently no new individual versions for MacOSX, Linux and Windows.
If the executable for your machine architecture does not work for you, 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) on Linux, 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.

References

TreeSnatcher Plus Poster

A TreeSnatcher Plus conference poster (Thomas Laubach and Martin J. Lercher)

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

Get the applications note here

If you are using TreeSnatcher Plus, please cite this article.

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

Benchmarks

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.

Tutorials

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.
TreeSnatcher Plus for Mac OS X uses Preview.app.
TreeSnatcher Plus for Linux uses its own PDF viewer.
TreeSnatcher Plus for Windows uses the default PDF viewer.
The tutorials are here