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Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.

Lucas Czech1, Pierre Barbera1, Alexandros Stamatakis1,2

  • 1Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany.

Bioinformatics (Oxford, England)
|February 5, 2020
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Summary

We introduce genesis, a C++ library, and gappa, a command-line tool, for efficient phylogenetic data analysis. These tools support phylogenetic trees, placements, and sequences, offering both simplicity and customizability for researchers.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Phylogenetic data analysis is crucial for understanding evolutionary relationships.
  • Existing tools may lack efficiency, customizability, or ease of use for diverse data types.

Purpose of the Study:

  • To present genesis, a C++ library for handling phylogenetic data.
  • To introduce gappa, a command-line tool for common phylogenetic analyses.
  • To provide efficient, customizable, and well-tested software for phylogenetic research.

Main Methods:

  • Development of genesis library in modern C++11.
  • Creation of gappa command-line tool.
  • Implementation of support for phylogenetic trees, placements, sequences, and taxonomies.

Main Results:

  • genesis and gappa offer high-level simplicity and low-level customizability.
  • The tools are computationally efficient and field-proven.
  • Both software are available under GPLv3 license.

Conclusions:

  • genesis and gappa provide a robust and versatile solution for phylogenetic data analysis.
  • The software is suitable for a wide range of users, from beginners to experts.
  • Open-source availability facilitates adoption and further development in the research community.