This website presents an algebraic classification of small tree and network models in phylogenetics. It currently hosts data on twentysix trees, paired with five different model types. These are listed in the table on the landing page. Mathematical details can be found on individual subpages for each tree and model. Never heard about algebraic phylogenetics? It is a subfield of Algebraic Statistics, with MSC identifiers 62R01, 65H10, 92D15, 68W30, and 14Q30. The page Notions and notation gives a mathematical introduction to the topic.

The content displayed on this website is work in progress! You can see its current version on the landing page and in the upper left hand corner: at the time of writing, it is version 0.1.

We focus on providing thorough computational proof for every result we display. To achieve this, the website is supplemented by the AlgebraicPhylogenetics.jl software. The code is part of the AlgebraicStatistics.jl package in the OSCAR project, written in Julia. OSCAR provides serialization. In the upcoming version 0.2 of this website, we use this technology to make our data available for immediate embedding into your own code. Until then, you can find code snippets on the AlgebraicPhylogenetics.jl software-documentation page linked above.

This website was set up and is currently maintained by Marina Garrote-López and Christiane Görgen, with the support of Tabea Bacher, Marius Neubert, and Luis David Garcia Puente.

The source code is available on GitHub under the MIT License. You can copy, use, and modify this project freely.

Want to contribute? Please do! You can join our team on GitHub by forking the repository this website is build on or our software package, modifying the content at your leisure, and sending us a pull request. The version displayed here is a frozen copy hosted at the gitlab instance of Max Planck Institute of Mathematics in the Sciences.

We prepared a report on technological and design decisions and lessons learned in setting up this project, both as a website, a software package, and as a sustainable, FAIR database. The preprint is under peer review and available on arxiv: https://arxiv.org/pdf/2501.10823

Want to contact us? Drop us an email: maintainers@algebraicphylogenetics.org

You may cite this database as follows.

  
  @online{smalltrees,
    author = {The algebraic-phylogenetics collaboration},
    title = {A database of small tress and networks in algebraic phylogenetics},  
    year = 2024,
    url = {http://www.algebraicphylogenetics.org},
    note = {Version 0.1}
  }
  
  

The design of this website was adapted to fit our needs from fanography.info courtesy of Pieter Belmans and thanks to Victor Zimmermann.

Tabea Bacher, Christiane Görgen, Marius Neubert, and Victor Zimmermann were supported by "MaRDI – Mathematische Forschungsdateninitiative" (Mathematical Research Data Initiative), funded by the Deutsche Forschungsgemeinschaft (DFG), Projektnummer 460135501. NFDI 29/1.

Marina Garrote-López was supported by the Max Planck Institute for Mathematics in the Sciences. Thomas Endler of that institute designed our header.

We are all highly indebted to the OSCAR group and their amazing ability to answer all requests and quickly adapt to our technical needs.