We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. MCMC-based methods are important for Bayesian inference of phylogeny and related parameters.
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