Moments and Stochastic Trees from Event Reactions
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.
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.