AsymmeTree

AsymmeTree is an open-source Python library for the simulation and analysis of phylogenetic scenarios. It includes a simulator for species and gene trees with heterogeneous evolution rates, nucleotide and amino acid sequences with or without indels, as well as whole genomes/proteomes.

Moreover, it includes a matplotlib-based visualization of the simulated trees as well as tools for the extraction of information from the simulated scenarios such as orthology, best matches, and xenology.

The library is primarily designed to explore and validate mathematical concepts, and to test inference methods for various steps on the way to more realistically-available data, i.e., dated gene trees, additive distances of gene sets, noisy distances and finally sequences.

Installation and usage

The package requires Python 3.10 or higher. The asymmetree package is available on PyPI:

pip install asymmetree

See also the page Installation in the documentation.

The AsymmeTree documentation contains a user manual with example code as well as the API reference.

If you want to contribute to the project, please see the contributing guidelines.

Citation

If you use AsymmeTree in your project or code from it, please consider citing:

David Schaller, Marc Hellmuth, and Peter F. Stadler. AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories. Software 2022, 1(3), 276-298; doi: 10.3390/software1030013

Please report any bugs and questions in the Issues section. Also, feel free to make suggestions for improvement and/or new functionalities.

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