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bModelTest

Bayesian model test package for BEAST 3.

Uses reversible-jump MCMC to switch between substitution models over nucleotide data, with or without gamma rate heterogeneity and/or invariant sites.

See the wiki for usage details.

Paper: Bouckaert, Remco R., and Alexei J. Drummond. "bModelTest: Bayesian phylogenetic site model averaging and model comparison." BMC evolutionary biology 17.1 (2017): 42.

Building from source

Requirements:

  • JDK 25 or later
  • Apache Maven 3.9+
mvn compile
mvn test

To run the bundled example:

mvn package -DskipTests
java --module-path "$BEAST3/beast-base/target/beast-base-2.8.0-SNAPSHOT.jar:$BEAST3/beast-base/target/lib:target/bModelTest-1.4.0-beta1.jar" \
     -m beast.base/beast.base.minimal.BeastMain examples/bModelTest.xml

(replace $BEAST3 with the path to your beast3 checkout).

To develop against an unreleased BEAST 3 SNAPSHOT, install BEAST 3 from source:

cd ~/Git/beast3
mvn install -DskipTests