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TreeRipper web application: towards a fully automated optical tree recognition software.

Joseph Hughes¹

¹IBAHCM, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, University Avenue, Glasgow, G12 8QQ, UK. joseph.hughes@glasgow.ac.uk

BMC Bioinformatics

|May 24, 2011

Summary

TreeRipper is a new website that automates the recognition of phylogenetic trees from images. This tool helps digitize historical evolutionary data for modern research, with 32% of tested images successfully processed.

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Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Phylogenetic trees have been a standard for representing evolutionary relationships for over a century.
Traditional methods of sharing phylogenetic hypotheses are becoming outdated with the advent of the internet.
There is a need for modern software to process and utilize published phylogenetic data.

Purpose of the Study:

To develop a website for the automated recognition of multifurcating phylogenetic trees.
To facilitate the digitization of historical phylogenetic data for 21st-century research.

Main Methods:

TreeRipper website utilizes a command-line C++ program for image analysis.
The software performs image cleaning, line detection, node label removal, and edge contour determination.

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Main Results:

TreeRipper successfully recognized 32% of images meeting its prerequisites.
The software can process multifurcating phylogenetic trees, with the largest processed tree having 115 leaves.
A dataset of 100 tree images and associated files is provided for future software development.

Conclusions:

TreeRipper represents a step towards automating the digitization of published phylogenies.
Despite challenges in diverse tree illustrations, automated recognition is becoming feasible.
The open-source nature and provided dataset encourage further development in phylogenetic data processing.