title: TreeRipper web application: towards a fully automated optical tree recognition software.
abstract: BACKGROUND
  Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century.
  
  
  RESULTS
  TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/). The program accepts a range of input image formats (PNG, JPG/JPEG or GIF). The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR) is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves.
  
  
  CONCLUSIONS
  Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.
authors: IBAHCM, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, University Avenue, Glasgow, G12 8QQ, UK. joseph.hughes@glasgow.ac.uk
authors: Joseph
authors: J
authors: Hughes
references: Br Foreign Med Chir Rev. 1860 Apr;25(50):367-404
references: 30164232
references: Syst Biol. 2006 Oct;55(5):818-36
references: 17060202
references: BMC Evol Biol. 2009 Feb 11;9:37
references: 19210768
references: Bioinformatics. 2007 Dec 15;23(24):3384-5
references: 17893085
references: BMC Bioinformatics. 2009 Oct 27;10:356
references: 19860910