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ReMASTER: improved phylodynamic simulation for BEAST 2.7.

Timothy G Vaughan1,2

  • 1Department of Biosystems Science and Engineering, ETH Zurich, Basel 4056, Switzerland.

Bioinformatics (Oxford, England)
|January 10, 2024
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Summary
This summary is machine-generated.

ReMASTER is a new package for BEAST 2 that simplifies the simulation of phylogenetic trees and population dynamics. This tool aids in developing and testing phylodynamic inference algorithms and assessing model adequacy.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Epidemiology

Background:

  • Phylodynamic models integrate phylogenetic trees with biological parameters like speciation, extinction, population size, migration, and transmission rates.
  • Simulating these trees and dynamics is crucial for developing inference algorithms, quantifying model-misspecification biases, and performing model adequacy assessments.

Purpose of the Study:

  • Introduce ReMASTER, a BEAST 2 package for specifying and simulating phylogenetic trees and population dynamics under phylodynamic models.
  • Provide a simple, efficient, and flexible approach for these simulations within the BEAST 2 framework.

Main Methods:

  • ReMASTER is implemented as a package for the BEAST 2 phylogenetic inference platform.
  • It facilitates the specification and simulation of phylodynamic models, enabling joint simulation and inference analyses.

Main Results:

  • ReMASTER offers improved efficiency, ease of use, and flexibility compared to its predecessor, MASTER.
  • Deeper integration with BEAST 2 enhances its utility for complex phylodynamic analyses.

Conclusions:

  • ReMASTER provides a valuable tool for researchers in phylodynamics, phylogeography, and epidemiology.
  • Its accessibility and enhanced features support the development and validation of phylodynamic models and inference methods.