Moments and Stochastic Trees from Event Reactions

Project maintained by Tim Vaughan

MASTER is a software package aimed at providing a general means of creating simulators for stochastic models of structured and unstructured population dynamics. It also supports the simulation of inheritance trees and networks under these same models.


MASTER is a BEAST 2 package and can therefore be installed easily from within BEAUti. Simply download and install the latest version of BEAST 2 from the web site, open BEAUti, then choose "File->Manage Packages" and select MASTER from the package list that appears. MASTER simulations can then be run by simply running BEAST and selecting the MASTER-specific XML input file.


For the full documentation of MASTER, please refer to the wiki. This includes a fuller discussion of the foundational goals of the software, a complete description of the XML input format and a set of tutorials aimed at getting new users up to speed as easily as possible.

Feedback, Feature Requests and Bug Reports

Feature requests and bug reports should be submitted via the project's issues page. Any other feedback can be addressed directly to Tim Vaughan.


If you use MASTER as part of research that leads to a publication, we ask that you cite the following article:

T. G. Vaughan and A. J. Drummond, "A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics", Mol. Biol. Evol. 30(6):1480, 2013. (link)


MASTER is an add-on to the fantastic BEAST 2 phylogenetics inference system. For ease of installation, BEAST 2 is currently bundled with the downloadable MASTER binary. We owe a great debt of thanks to the BEAST 2 developers for creating such a wonderfully extensible system.

Work on this project is made possible by generous funding from the
Allan Wilson Centre for Molecular Ecology and Evolution.