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RootAnnotator computes root posterior probabilities. For this, it makes use of posterior collections of trees generated under clock models (e.g. .nexus files such as those generated by BEAST or MrBayes), from which branches wearing the root are identified and counted. It can annotate root posteriors on different types of summary trees, including maximum clade credibility trees (MCC trees). It can also create a file for Tracer to visualize the convergence of root posteriors.
It should be noted that RootAnnotator generate MCC trees by running TreeAnnotator (distributed with BEAST; https://code.google.com/p/beast-mcmc/).
Citation: Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY. Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage. PLOS Currents Outbreaks. 2014 Jun 16. Edition 1. doi: 10.1371/currents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86.
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