morph-models

Models for discrete morphological character data in BEAST 3.

Implements the Lewis MK and MKv substitution models (Lewis, 2001), along with ordinal and nested ordinal variants for ordered character data.

Substitution models

Class	Description
LewisMK	Equal or user-specified frequency Mk model
Ordinal	Tridiagonal rate matrix for ordered characters
NestedOrdinal	Nested ordinal rate matrix (state 0 transitions to all others)

Building

BEAST 3 dependencies are resolved from Maven Central — no extra configuration needed.

mvn compile
mvn test

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

cd ~/Git/beast3
mvn install -DskipTests

Running

# Validate an XML
mvn exec:exec -Dbeast.args="-validate examples/M3982.xml"

# Run an analysis
mvn exec:exec -Dbeast.args="-overwrite examples/M3982.xml"

Examples

• examples/M3982.xml — Anolis lizard morphological analysis using BEAST 3 spec classes
• examples/legacy-2.7/ — original BEAST 2.7 XML files (some require external packages)

Releasing

ZIP / CBAN

The release.sh script builds a BEAST package ZIP and optionally creates a GitHub release for submission to CBAN:

./release.sh            # build ZIP only
./release.sh --release  # build ZIP + create GitHub release

Maven Central

Pushing a v* tag triggers the CI workflow to publish to Maven Central.

BEAST 3 users can then install with:

Package Manager > Install from Maven > io.github.compevol:morph-models:1.3.0-beta2

Or from the command line:

packagemanager -maven io.github.compevol:morph-models:1.3.0-beta2

References

Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50(6), 913–925.