TreeSnatcher plus: capturing phylogenetic trees from images

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• 作者：Thomas Laubach (1)
  Arndt von Haeseler (2) (3) (4)
  Martin J Lercher (1)
  
• 关键词：Newick format ; Phylogenetic tree recognition ; Image digitization ; Phylogeny preservation
• 刊名：BMC Bioinformatics
• 出版年：2012
• 出版时间：December 2012
• 年：2012
• 卷：13
• 期：1
• 全文大小：290KB
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• 作者单位：Thomas Laubach (1)
  Arndt von Haeseler (2) (3) (4)
  Martin J Lercher (1)
  
  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
  
• ISSN：1471-2105

文摘

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.