contraband

The 'contraband' (continuous traits brownian models) BEAST 2 package provides a suite of models for the study of continuous trait evolution in a Bayesian framework.

Citation

[ref] Théo Gaboriau, Fábio K. Mendes, Simon Joly, Daniele Silvestro and Nicolas Salamin (2020). A multi-platform package for the analysis of intra- and interspecific trait evolution. Methods Ecol. Evol., 1-9.

Building

contraband can be installed through BEAUti or the BEAST 2 package manager.

In order to build an executable .jar file for the contraband package:

• (1) Clone and build dependencies:

  • (1.1) BEAST2 from here;
  • (1.2) beast-outercore from here;
  • (1.3) BEASTLabs from here;
  • (1.4) sampled-ancestors from here;

• (2) Clone the contraband repository side-by-side with the dependencies' (above) directories resulting from step (1);

• (3) From contraband/, type:

  $ ant
  

  This command invokes the ant tool, which executes the building instructions inside build.xml. The new contraband .jar file will be put inside build/dist/.

Running an analysis with contraband

From your shell or Terminal, type:

$ /path/to/build/dist/contraband.v0.0.1.jar /path/to/contraband/examples/testing/BMMVNLikelihoodOneTrait_fixedtree.xml