The documentation of genesis has two main parts: The User Manual and the API Reference.

Important remark: genesis is under active development. The manual is not yet exhaustive, the API might change with subsequent releases, there might be functions missing that you consider essential, and of course, there might be bugs. Please report all issues on our GitHub page. Your feedback is highly appreciated!

User Manual

The manual contains high level explanations, tutorials and code examples for the functionality of genesis. It is intended for end users who want to use existing scripts and applications, and for getting started with genesis.

Furthermore, see the Supplement for additional information.

API Reference

The documentation of the application programming interface (API) is intended for users who want to use genesis as a library or toolkit for their own applications. It provides detailed references for the symbols defined in genesis:

Support

For bug reports and feature requests in genesis, please open an issue on our GitHub page.

For user support on phylogenetic placement topics, please see our Phylogenetic Placement Google Group. It is intended for discussions about phylogenetic placement, and for user support for our software tools such as EPA-ng and Gappa.

Citation

When using Genesis, please cite

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.
Lucas Czech, Pierre Barbera, and Alexandros Stamatakis.
Bioinformatics, 2020. https://doi.org/10.1093/bioinformatics/btaa070

Also, see Gappa for our command line tool to run your own analyses of phylogenetic placement data.

Acknowledgements

This work is financially supported:

2014-2019: Klaus Tschira Foundation and HITS gGmbH - Heidelberg Institute for Theoretical Studies in Heiderberg, Germany.
2020-2021: Carnegie Institution For Science in Stanford, USA.

See Acknowledgements for the full list of acknowledgements, particularly for dependencies. See the webpages of the Exelixis Lab and the Moi Lab for our other projects.

License

Genesis - A toolkit for working with phylogenetic data.
Copyright (C) 2014-2021 Lucas Czech

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Contact:

2014-2019:
Lucas Czech, lucas.czech@h-its.org
Exelixis Lab, Heidelberg Institute for Theoretical Studies
Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany

2020-2021:
Lucas Czech, lczech@carnegiescience.edu
Department of Plant Biology, Carnegie Institution For Science
260 Panama Street, Stanford, CA 94305, USA