ReMASTER: Improved phylodynamic simulation for BEAST 2.7

Abstract

SummaryPhylodynamic models link phylogenetic trees to biologically-relevant parameters such as speciation and extinction rates (macroevolution), effective population sizes and migration rates (ecology and phylogeography), and transmission and removal/recovery rates (epidemiology) to name a few. Being able to simulate phylogenetic trees and population dynamics under these models is the basis for (a) developing and testing of phylodynamic inference algorithms, (b) performing simulation studies which quantify the biases stemming from model-misspecification, and (c) performing so-called model adequacy assessments by simulating samples from the posterior predictive distribution. Here I introduce ReMASTER, a package for the BEAST 2 phylogenetic inference platform which provides a simple and efficient approach to specifying and simulating the phylogenetic trees and population dynamics arising from phylodynamic models. ReMASTER is a complete rewrite of an earlier package, MASTER, and boasts improved efficiency, ease of use, flexibility of model specification, and integration with BEAST 2. Availability and ImplementationReMASTER can be installed directly from the BEAST 2 package manager, and its documentation is available online at https://tgvaughan.github.io/remaster. ReMASTER is free software, and is distributed under version 3 of the GNU General Public License. The Java source code for ReMASTER is available from https://github.com/tgvaughan/remaster.