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.

Modules

• beast-morph-models — core substitution models and alignment classes (depends on beast-base)
• beast-morph-models-fx — BEAUti integration (depends on beast-fx)

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 GitHub Packages (or Maven Central, if published there). For GitHub Packages, add a personal access token (classic) with read:packages scope to ~/.m2/settings.xml:

<settings>
  <servers>
    <server>
      <id>github</id>
      <username>YOUR_GITHUB_USERNAME</username>
      <password>YOUR_GITHUB_PAT</password>
    </server>
  </servers>
</settings>

Then build morph-models:

cd ~/Git/morph-models
mvn compile
mvn test -pl beast-morph-models

Alternatively, you can install BEAST 3 from source (no GitHub auth needed):

cd ~/Git/beast3
mvn install -DskipTests

Running

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

# Run an analysis
mvn -pl beast-morph-models 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 existing 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

mvn clean deploy -Prelease

This builds the JARs (with version.xml embedded for service discovery), generates sources and javadoc JARs, signs everything with GPG, and uploads to Maven Central.

BEAST 3 users can then install with:

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

Or from the command line:

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

References

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