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Open Access Highly Accessed Software

TreeSnatcher plus: capturing phylogenetic trees from images

Thomas Laubach1*, Arndt von Haeseler234 and Martin J Lercher1

Author Affiliations

1 Department of Bioinformatics, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, Duesseldorf 40225, Germany

2 Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Dr-Bohr-Gasse 9, Vienna, Austria

3 University of Vienna, Vienna, Austria

4 Medical University Vienna, Vienna, Austria

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BMC Bioinformatics 2012, 13:110  doi:10.1186/1471-2105-13-110

Published: 24 May 2012

Abstract

Background

Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.

Results

TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees.

Conclusions

Although illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format.

Keywords:
Newick format; Phylogenetic tree recognition; Image digitization; Phylogeny preservation