beast-pype 0.1.0

A package of BEAST 2 pipelines for phylodynamics.

(Français)

BEAST_pype: An automated pipeline for high throughput phylodynamic analyses using BEAST 2.

BEAST_pype is a pipeline with aim of automating and parallelizing many of the steps involved in phylodynamics using BEAST 2. The workflows expedite phylodynamic analyses using BEAST 2 via a series of python-based Jupyter Notebooks.

BEAST_pype was concieved with the aim to speed up and automate the use of BEAST 2 analyses for routine public health use at the Public Health Agency of Canada.
Activities include running routine analyses on continuously circulating viruses, such as SARS-CoV-2 or Influenza, to extract epidemiological parameters of interest for surviellance. Also, for accelerating research or outbreak investigations that require several experimental runs for optimization and more rapid results generation.

Features of BEAST_pype include:

• Command-line launchable, and Yaml file controlled pipeline.
• Improved XML generation and re-use. e.g. using user-provided BEAST-2 xmls as a template for generating a new BEAST-2 xml from new sequences with the associated metadata.
• Launching several parallelized runs and a GUI for selecting converged MCMC chains.
• Automated generation of reports analysing BEAST 2 runs (diagnostic and result plots and statistics).
• Ability to create and include initial trees for faster runs.
• Incorporating downsampling techniques.

For instructions, getting started, and more details, please see BEAST_pype's wiki.

IMPORTANT NOTES

• With this early access version of beast_pype the beast_pype python package is installed with the -e flag. This means it is intsalled in an editable development mode. MEANING IF YOU MAKE ANY CHANGES TO THE FILES IN src/beast_pype THIS WILL AFFECT YOUR beast_pype INSTALLATION
• For ease of distribution reasons beast_pype uses the version of BEAST 2 that is available via conda, specifically bioconda, 2.6 as 2025-Jun-25. Template beast2 xmls from other versions of may not work. BEAST 2.7.7 is available on the conda channel millerjeremya. However, I tested this on a Linux OS (2025-06-04) and could not get the command line arguments to work.

Installation instructions:

See the wiki's installation instructions section.

Guides on Running BEAST_pype Workflows

The documentation for running BEAST_pype's workflows is in the repo's wiki.

How to Contribute

See CONTRIBUTING.md

Legal

Copyright (c) His Majesty the King in Right of Canada, as represented by the Minister of Health, 2025.

Unless otherwise noted, the source code of this project is covered under Crown Copyright, Government of Canada, and is distributed under the GPL-2 license.

The Canada wordmark and related graphics associated with this distribution are protected under trademark law and copyright law. No permission is granted to use them outside the parameters of the Government of Canada's corporate identity program. For more information, see Federal identity requirements.

Contributors

Martin Grunnill [e-mail]
Carmen Lia Murall [e-mail]
Rachelle Di Tullio
Kodjovi Mlaga

Acknowledgments

Useful Software

A forerunner and inspiration of this work was CoV flow.

BEAST_pype would not be possible without:

• BEAST 2 also Bouckaert R. et al. (2019)
• The initial work on BEAST2xml by Terry Jones.

Feedback During Development

George Long
Venketa Duvvuri
Louis Du Plessis
Samuel Alizon
Remco Bouckaert Gonche Danesh

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Voir CONTRIBUTING.md

Licence

Sauf indication contraire, le code source de ce projet est protégé par le droit d'auteur de la Couronne du gouvernement du Canada et distribué sous la licence GPL-2.

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