CoupledMCMC is a BEAST 2 package, which you can install through the package manager that comes with BEAST. Choose CoupledMCMC from the list of packages.

If you want to run a Standard analysis (i.e. an analysis using the Standard template for MCMC analyses), you can choose the CoupledMCMC template instead under the File => Templates => CoupledMCMC menu. Then you can set up the analysis as you would a Standard analysis, except the MCMC tab is replaced by the CoupledMCMC tab.

If you want to run another analysis than a Standard one, you still can use CoupledMCMC per below.

After you installed the CoupledMCMC package (version 0.1.5 or better), the MCMC2CoupledMCMC app becomes available in the app launcher.

1. Create MCMC analysis in BEAUti with any of the available templates, save as mcmc.xml

Now there are 2 ways to proceed:

2a. from a terminal, run

/path/to/beast/bin/applauncher MCMC2CoupledMCMC -xml mcmc.xml -o mc3.xml

This creates a file mc3.xml containing a CoupledMCMC analysis with the same model/operators/loggers etc as the mcmc.xml analysis.

2b. from BEAUti, use menu File > Launch apps, select MCMC to Coupled MCMC converter from the available apps, fill in form and click OK

In order to set up a pre-prepared xml to run with coupled MCMC, open the *.xml and change the MCMC line in the xml.

To do so, go to the line with:

<run id="mcmc" spec="MCMC" chainLength="....." numInitializationAttempts="....">

To have a run with coupled MCMC, we have to replace that one line with:

<run id="mcmc" spec="beast.coupledMCMC.CoupledMCMC" chainLength="100000000" storeEvery="1000000" deltaTemperature="0.025" chains="2" resampleEvery="10000">

• chainLength="100000000" defines for how many iterations the chains is run
• deltaTemperature="0.025" defines the temperature difference between the chain n and chain n-1. This value should be changed such that the acceptance probability of a swap is between 0.25 and 0.6
• chains="2" defines the number of parallel chains that are run. The first chain is the one that explores the posterior just like a normal MCMC chain. All other chains are what's called heated. This means that MCMC moves of those chains have a higher probability of being accepted. While these heated chains don't explore the posterior properly, they can be used to propose new states to the one cold chain.

Müller, Nicola Felix, and Remco Bouckaert. "Coupled MCMC in BEAST 2." bioRxiv (2019): 603514. (abstract, pdf);

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference https://academic.oup.com/bioinformatics/article/20/3/407/186341