/asm

Automatically Stopping MCMC/MC3

Primary LanguageJava

ASM: Auto Stopping MCMC/MC3

ASM package for BEAST 2

ASM is a package that allows MCMC to stop automatically instead of having run till an arbitrary number a samples have been obtained. This makes it more convenient to set up and run an analysis.

Installing the ASM package

To install ASM, start BEAUti

  • choose menu File => Manage packages
  • Select ASM from the list of packages by clicking on it in the list. If ASM is not in the list, add the package-extra-2.7 repository, which you can do in BEAUti through button Package Repositories then click Add URL then add https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra-2.7.xml in the entry and click OK. Then click Close and the package should appear in the list (together with a few other experimental packages).
  • click the Install button.

Restart BEAUti before using the package.

Using the ASM package

Set up the analysis as per usual for an MCMC analysis, then go the the MCMC tab. From the drop-down box select Automatic Stopping MCMC, and a number MCMC options disappear and are replaced by ASM options.

asm

You can set parameters by clicking the TreePSRF button for the Gelman-Rubin-like criterion or TraceESS button for the trace-ESS criterion.

asm

Paper

If you publish a paper using this package, please cite
Lars Berling, Remco Bouckaert, and Alex Gavryushkin
Automated convergence diagnostic for phylogenetic MCMC analyses
BioRxiv 2023
https://doi.org/10.1101/2023.08.10.552869