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Abstract
BackgroundFigures 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.ResultsTreeSnatcher 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.ConclusionsAlthough 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.
Highlights
Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses
The program TreeRipper by Joseph Hughes [5] automatically converts images of rectangular trees that fulfil a strict set of criteria into the Newick format
An image that shows a uniformly dark, rectangular phylogenetic tree on a uniformly light background in sufficient resolution, without foreground elements overlapping with the tree, will need almost no preprocessing
Summary
Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. Every scientific field that processes information with the aid of computers needs to maintain and preserve its technical illustrations in a machine-readable fashion for later reuse. No computer program can automatically convert arbitrarily shaped phylogenetic trees from an illustration into a machine-readable expression, e.g., the Newick format [1]. The styles in which phylogenetic trees have been published are as TreeSnatcher Plus (Figure 1) is not the first program aimed at the digitization of phylogenies. In 2007, we presented TreeSnatcher [4], an application that identified the topology of an arbitrarily shaped tree (e.g., a figure from a publication) semi-automatically with user interaction. The program TreeRipper by Joseph Hughes [5] automatically converts images of rectangular trees that fulfil a strict set of criteria into the Newick format. TreeRipper’s success rate is relatively low, with only about one third of sample images converted correctly [5]
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