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Sampled Ancestors

Build Status

This BEAST 3 package provides MCMC proposals and post-processing tools for samples of trees containing sampled ancestors. It relies on the support for sampled-ancestor trees built into the beast.base.evolution.tree.Tree class.

The paper describing this package is:

Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond (2014) Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. PLoS Computational Biology https://doi.org/10.1371/journal.pcbi.1003919

Building from source

Requirements:

  • JDK 25 or later
  • Apache Maven
mvn compile

To run an example:

mvn -pl beast-sampled-ancestors exec:exec -Dbeast.args="examples/bears.xml"

Project structure

This is a multi-module Maven project with two modules:

  • beast-sampled-ancestors — core module (no JavaFX dependency, runs headless on clusters)
  • beast-sampled-ancestors-fx — BEAUti input editors and JavaFX-dependent tools

sa.app.simulators

Simulators for the fossilized birth-death (FBD) model and FBD-skyline model.

sa.app.tools

  • Conversion tools between zero-branch-length sampled-ancestor trees and native sampled-ancestor trees
  • SATreeTraceAnalysis and various other post-processing tools (in -fx module)

sa.evolution.operators

Operators that permit MCMC on sampled-ancestor trees.

sa.evolution.speciation

SpeciesTreeDistribution calculations for the FBD prior:

  • SABirthDeathModel — FBD prior with multiple hard-coded parameterizations
  • ParameterizedSABirthDeathModel — FBD prior with object-oriented parameterizations

sa.beauti (in -fx module)

BEAUti input editors for sampled-ancestor priors.

fxtemplates (in -fx module resources)

Contains FBD.xml, a BEAUti template for SABirthDeathModel and sampled-ancestor tree operators. Located at beast-sampled-ancestors-fx/src/main/resources/sa.fx/fxtemplates/.

License

This software is free (as in freedom). With your modified versions provided you extend the same courtesy to users of your modified version. Specifically, it is made available under the terms of the GNU General Public License version 3.

Acknowledgements

Work on this project was supported by: