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.
Single Maven artifact: io.github.compevol:sampled-ancestors. JPMS module: sampled.ancestors.
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
Requirements:
- JDK 25 or later
- Apache Maven
mvn compileTo run an example:
mvn exec:exec -Dbeast.args="examples/bears.xml"To launch BEAUti:
mvn exec:exec -Dbeast.module=beast.fx -Dbeast.main=beastfx.app.beauti.BeautiSimulators for the fossilized birth-death (FBD) model and FBD-skyline model.
Conversion tools between zero-branch-length sampled-ancestor trees and native sampled-ancestor trees.
SATreeTraceAnalysis and various other post-processing tools.
Operators that permit MCMC on sampled-ancestor trees.
SpeciesTreeDistribution calculations for the FBD prior:
SABirthDeathModel-- FBD prior with multiple hard-coded parameterizationsParameterizedSABirthDeathModel-- FBD prior with object-oriented parameterizations
BEAUti input editors for sampled-ancestor priors.
Contains FBD.xml, a BEAUti template for SABirthDeathModel and sampled-ancestor tree operators.
Located at src/main/resources/sampled.ancestors/fxtemplates/.
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.
Work on this project was supported by:
- The Royal Society of New Zealand's Marsden Fund grant contract UOA1324
- The University of Auckland