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Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data

View ORCID ProfileLucas Czech, View ORCID ProfilePierre Barbera, View ORCID ProfileAlexandros Stamatakis
doi: https://doi.org/10.1101/647958
Lucas Czech
aComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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  • ORCID record for Lucas Czech
  • For correspondence: lucas.czech@h-its.org alexandros.stamatakis@h-its.org
Pierre Barbera
aComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
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Alexandros Stamatakis
aComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
bInstitute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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  • ORCID record for Alexandros Stamatakis
  • For correspondence: lucas.czech@h-its.org alexandros.stamatakis@h-its.org
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Summary

We present GENESIS, a library for working with phylogenetic data, and GAPPA, an accompanying command line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies, and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested, and field-proven.

Availability and Implementation Both GENESIS and GAPPA are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa.

Contact lucas.czech{at}h-its.org and alexandros.stamatakis{at}h-its.org.

Footnotes

  • Revision following the suggestions of the review of our submission at OUP Bioinformatics.

  • https://github.com/lczech/genesis

  • https://github.com/lczech/gappa

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 01, 2019.
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Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data
Lucas Czech, Pierre Barbera, Alexandros Stamatakis
bioRxiv 647958; doi: https://doi.org/10.1101/647958
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Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data
Lucas Czech, Pierre Barbera, Alexandros Stamatakis
bioRxiv 647958; doi: https://doi.org/10.1101/647958

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