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MASCOT

MASCOT (Marginal Approximation of the Structured Coalescent) is a BEAST 3 package for efficient phylogeographic inference under the structured coalescent.

A tutorial on how to use MASCOT can be found here.

Maven coordinates

<dependency>
    <groupId>io.github.compevol</groupId>
    <artifactId>mascot</artifactId>
    <version>3.1.0-beta1</version>
</dependency>

JPMS module name: mascot

Building from source

Requires Java 25 and Maven.

mvn install -DskipTests

Running BEAST with Mascot

mvn exec:exec -Dbeast.args="-overwrite examples/Constant.xml"

Citation

Müller NF, Bouckaert RR, Wu C-H, Bedford T. MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions. PLOS Computational Biology 21(9):e1013421, 2025. DOI:10.1371/journal.pcbi.1013421

Müller NF, Dudas G, Stadler T. Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations. Virus Evolution 5(2):vez030, 2019. DOI:10.1093/ve/vez030

Müller NF, Rasmussen DA, Stadler T. MASCOT: parameter and state inference under the marginal structured coalescent approximation. Bioinformatics 34(22):3843–3848, 2018. DOI:10.1093/bioinformatics/bty406

Müller NF, Rasmussen DA, Stadler T. The Structured Coalescent and Its Approximations. Molecular Biology and Evolution 34(11):2970–2981, 2017. DOI:10.1093/molbev/msx186

License

The java source code is licensed under the GNU General Public License v3.0.