A toolkit for working with phylogenetic data.
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genesis Documentation

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

Important remark: genesis is under active development and quite young. 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:


For user support, please see our Phylogenetic Placement Google Group. It is intended for discussions about phylogenetic placement, and for user support for our software tools. You can also find support for EPA-ng and Gappa there.

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


Currently, there is no publication to be cited. This is unfortunate and will hopefully change. Until then, please write an email to lucas.czech@h-its.org to ask for instructions.


This work is financially supported by the Klaus Tschira Foundation and the HITS gGmbH - Heidelberg Institute for Theoretical Studies.

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


Genesis - A toolkit for working with phylogenetic data.
Copyright (C) 2014-2016 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/.

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