ReMASTER

ReMASTER simulates phylogenetic trees and population dynamics under phylodynamic models within the BEAST 2 platform.

Key Features:

• Phylodynamic model support: Simulates phylogenetic trees under birth-death and coalescent models.
• Population dynamics simulation: Generates population dynamics arising from phylodynamic models.
• BEAST 2 integration: Functions as a package within BEAST 2, enabling joint simulation and inference analyses.
• Model specification flexibility: Provides efficient methods for specifying phylodynamic models.

Scientific Applications:

• Inference algorithm development and testing: Provides simulated data for developing and testing phylodynamic inference algorithms.
• Model misspecification analysis: Enables simulation studies that quantify biases from model misspecification.
• Model adequacy assessment: Supports posterior predictive distribution simulation for model adequacy assessments.
• Macroevolutionary dynamics: Simulates phylogenetic trees linked to speciation and extinction rates.
• Ecology and phylogeography: Simulates trees linked to effective population sizes and migration rates.
• Epidemiological dynamics: Simulates trees linked to transmission and removal/recovery rates.

Methodology:

ReMASTER is implemented as a Java package for BEAST 2.7, completely rewritten from the earlier MASTER package.