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Treeripper

Introduction

TreeRipper is a command line c++ program for the fully-automated recognition of multifurcating phylogenetic trees.

Installation

TreeRipper has a number of dependencies. First you will need to install the Magick++ library. Magick++ is included as part of ImageMagick source releases and may be retrieved here: http://www.imagemagick.org/script/download.php It is recommended to install ImageMagick for MacosX using Macport as it installs all the delgate libraries.

Secondly, you will need tesseract-ocr which can be found here: http://code.google.com/p/tesseract-ocr/

On Mac OS X, tesseract depends on libpng which itself needs zlib to compile. You will find them here: http://www.libpng.org/pub/png/libpng.html http://www.zlib.net/

Finally, to compile TreeRipper: 

cd src
make

To use TreeRipper: 

treeripper inputimage.jpg outputtree.nex

On Windows, matters are made slightly easier as Windows executables exist for tesseract.

Prerequisites

  • The current version of TreeRipper opens tree-image files in the formats PNG, JPG/JPEG, GIF, TIFF or PDF.
  • The tree needs to have the root on the left and leaves on the right.
  • Horizontal branches.
  • The tree constitutes a dark foreground on a light homogenous background (no background boxes or shading).
  • The tree must be bi- or multifurcating (not a network)
  • The inner nodes are branching points between lines and have no circles, rectangles, etc. inscribed.
  • Tip leaves must have branch lengths greater than 0.