TAMING THE BEAST

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The analysis will take about 10 minutes to complete. Read through the next section while waiting for your results or start preparing the XML file for the birth-death skyline analysis. The Coalescent Bayesian Skyline parameterization In the Partitions panel, import the nexus file with the alignment by navigating to File > Import Alignment in the menu and then finding the hcv.nexus file on your computer or simply drag and drop the file into the BEAUti window.

In this tutorial we will estimate the dynamics of the Egyptian Hepatitis C epidemic from genetic sequence data collected in 1993. To change the number of segments we have to navigate to the Initialialization panel, which is by default not visible. Navigate to View > Show Initialization Panel to make it visible and navigate to it ( Figure 7).

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where the argument after N is the particleCount you specified in the XML, and xyz.log the trace log produced by the NS run. Why are some NS runs longer than others?

We also identified some issues with a few of the tutorials during the workshop and I’ll also be updating them soon as well.So, the main parameters of the algorithm are the number of particles N and the subChainLength. N can be determined by starting with N=1 and from the information of that run a target standard deviation can be determined, which gives us a formula to determine N (as we will see later in the tutorial). The subChainLength determines how independent the replacement point is from the point that was saved, and is the only parameter that needs to be determined by trial and error – see FAQ for details. Get to know the advantages and disadvantages of the Coalescent Bayesian Skyline Plot and the Birth-Death Skyline.