sampled-ancestors

This BEAST 2 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.evolution.tree.Tree class (https://github.com/CompEvol/beast2/blob/master/src/beast/evolution/tree/Tree.java).

This archive contains the source code of the package and is therefore of primary interest to programmers.

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

Currently the sampled-ancestors package uses beast.* Java package namespace, which is now deprecated because the beast.* package namespace is reserved for the beast2 core (https://github.com/CompEvol/beast2).

Building package from source

To build this package from source, ensure you have the following installed:

• OpenJDK version 17 or greater
• A recent version of OpenJFX
• The Apache Ant build system
• An internet connection The internet connection is required since the build script downloads the most recent version of the BEAST 2 source to build the package against.

Assuming both Java and Ant are on your execution path and your current working directory is the root of directory this archive, simply type

sh JAVA_FX_HOME=/path/to/openjfx/ ant

from the command line to build the package. This may take up to a minute due to the script fetching the BEAST source, and the resulting binary will be left in the /dist directory.

To run the unit tests, use "ant test".

Archive Contents

• README.md : this file
• build.xml : Ant build script
• /doc : Contains additional documentation, currently a tutorial for using fossilized birth-death tree prior.
• /examples : Example analyses in beast2 xml format. See below for details.
• /src : source files. See below for details.
• /test : unit tests
• /templates : BEAUti templates. See below for details.
• version.xml : BEAST package version file.

The main Java packages and folders in the sampled-ancestors BEAST2 package are:

beast.app.simulators

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

beast.app.tools

• Contains conversion tools between zero-branch-length sampled-ancestor trees and native sampled-ancestor trees
• Contains SATreeTraceAnalysis and various other post-processing tools and support

beast.evolution.operators

• Contains the operators that permit MCMC on sampled-ancestor trees

beast.evolution.speciation

Contains SpeciesTreeDistribution calculations for the FBD prior:

• SABirthDeathModel - A species tree probability density of FBD prior with multiple hard-coded parameterizations possible.
• ParameterizedSABirthDeathModel - A species tree probability density with multiple parameterizations implemented in an object-oriented way.

templates

Contains a template called FBD.xml which provides a template for SABirthDeathModel and sampled-ancestor tree operators.

License

This software is free (as in freedom). You are welcome to use it, modify it, and distribute 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:

• The Royal Society of New Zealand's Marsden Fund grant contract UOA1324
• The University of Auckland