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.
<dependency>
<groupId>io.github.compevol</groupId>
<artifactId>mascot</artifactId>
<version>3.1.0-beta1</version>
</dependency>JPMS module name: mascot
Requires Java 25 and Maven.
mvn install -DskipTestsmvn exec:exec -Dbeast.args="-overwrite examples/Constant.xml"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
The java source code is licensed under the GNU General Public License v3.0.