⚠️ Package in active developement
If you encounter a bug or don't find documentation for something please raise an issue.

tetres

This is the development version 1.0.0 of the package tetres (TimE TREe Statistics). The submodule trees contains the data structures to work with discrete time trees, i.e. RNNI trees, and contains the distance implementation. The submodule summary contains implementations of the centroid algorithm, a version of Sturms algorithm (Fréchet mean) and an annotaion method for RNNI trees.

Installation

Download this Github repository, go into a command line and cd to the directories .../path/tetres/{trees, judgment}/ and run the make command in each (OpenMP is required for these c extensions).

Then this package can be installed for Python with

pip install -e your/path/to/tetres

For usage check out the documentation also availabe as a pdf.
Tutorials for specific tasks are available at tetres-tutorials.

References

If you publish a paper using the summary subpackage, please cite
Lars Berling, Lena Collienne, and Alex Gavryushkin
Estimating the mean in the space of ranked phylogenetic trees
bioRxiv 2023
https://doi.org/10.1101/2023.05.08.539790

If you publish a paper using the judgement (GR tree diagnostic) subpackage, please cite
Lars Berling, Remco Bouckaert, and Alex Gavryushkin
Automated convergence diagnostic for phylogenetic MCMC analyses
bioRxiv 2023
https://doi.org/10.1101/2023.08.10.552869

License

bioDS/tetres

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