tochsner / bdmm-prime

Modified implementation of the BDMM multi-type birth-death model for BEAST 2.

BDMM-Prime

The BDMM-Prime project provides a BEAST 2 package for performing phylodynamic inference under both structured and unstructured birth-death models.

The BDMM-Prime project is a fork of the original BDMM project. The intention is to extend the functionality of the original package, while improving its flexibility and ease of use. It incorporates the following enhancements:

• an improved BEAUti interface that allows a much more diverse range of analyses to be configured,
• automatic fall-back to analytical solutions for unstructured (single type) analyses,
• use of stochastic mapping for sampling ancestral states,
• a particle filtering algorithm allowing joint sampling of population trajectories,
• a heavily refactored code base intended to make the package easier to use, extend and maintain.

As a result of the many changes that were required in making this transition, BDMM-Prime is completely incompatible with BDMM itself. Thus the original package will be maintained separately to ensure that BEAST 2 XMLs and packages that depend on it remain usable.

BDMM-Prime is currently still in development and is not yet ready for general use. Instead, refer to the original BDMM project.

However, if you are interested in playing around with the new version, you can install it by adding https://tgvaughan.github.io/BDMM-Prime/package.xml as a third party BEAST package repository and installing the package that appears.

About the Name

"BDMM-Prime" is named according to the mathematical convention of using, for example, x' (read "x prime") to name an alternative variable which is in some sense related to x, but is nevertheless independent.

Importantly, it is not our intention to suggest that BDMM-Prime is superior to BDMM - just different.

Building from Source

To build BDMM-Prime from source you'll need the following to be installed:

• OpenJDK version 17 or greater
• A recent version of OpenJFX
• the Apache Ant build system

Once these are installed and in your execution path, issue the following command from the root directory of this repository:

JAVA_FX_HOME=/path/to/openjfx/ ant

The package archive will be left in the dist/ subdirectory.

Note that unless you already have a local copy of the latest BEAST 2 source in the directory ../beast2 and the latest BeastFX source in the directory ../beastfx relative to the BDMM-Prime root, the build script will attempt to download them automatically. Thus, most builds will require a network connection.

Acknowledgements

As this is a fork of BDMM, BDMM-Prime owes its existence to the authors and contributors of that project, in particular Denise Kühnert and Jérémie Scire.

If you use this package as part of your research, please cite the original BDMM paper:

• Kühnert, et al., "Phylodynamics with Migration: A ComputationalFramework to Quantify Population Structure from Genomic Data", MBE, 33:8, 2102-2116 (2016), doi:10.1093/molbev/msw064.

License

BDMM-Prime is free software. It is distributed under the terms of version 3 of the GNU General Public License. A copy of this license should be found in the file COPYING located in the root directory of this repository. If this file is absent for some reason, it can also be retrieved from https://www.gnu.org/licenses.