BDMM-Flow is a BEAST 2 package for performing phylodynamic inference under multi-type birth-death models.
The package is heavily inspired by and designed to be a drop-in replacement for the BDMM-Prime package. BDMM-Flow implements the same model but uses a flow-based representation of the model likelihood. This representation is faster for large trees and was introduced in the following paper:
- Stilianos Louca, Matthew W Pennell, A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models, Systematic Biology, Volume 69, Issue 3, May 2020, Pages 545–556, doi.org/10.1093/sysbio/syz055
This package adds additional modifications to the algorithm in order to further improve the performance. See the report in the supplementary repository for more details.
To try out BDMM-Flow, add https://raw.githubusercontent.com/tochsner/BDMM-Flow/main/version.xml as a third-party BEAST package repository and install the package that appears (see this article for more information).
To build BDMM-Flow from source, you need to install the following dependencies:
- OpenJDK version 17 or greater
- the Apache Ant build system
Once these are installed and in your execution path, you can build the package by simply running the following command:
antThis package is heavily inspired by the BDMM-Prime package developed by Tim Vaughan. BDMM-Prime in turn is a fork of the original BDMM package by Denise Kühnert and Jérémie Scire.
The flow algorithm was developed by Louca and Pennell in this paper:
- Stilianos Louca, Matthew W Pennell, A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models, Systematic Biology, Volume 69, Issue 3, May 2020, Pages 545–556, doi.org/10.1093/sysbio/syz055
Supplementary material like benchmarks and runtime analyses can be found in the supplementary repo.
BDMM-Flow 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.