11_Bayeslab

11_Bayeslab - Integrative Biology 200A PRINCIPLES OF...

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Integrative Biology 200A University of California, Berkeley PRINCIPLES OF PHYLOGENETICS Spring 2008 Lab 11: MrBayes Lab Introduction MrBayes uses a Markov Chain Monte Carlo (MCMC) approach to search for trees. There are two phases in an MCMC. The first phase, called “burn-in”, is more like a normal heuristic search in which the program explores the parameter space trying to find parameter values near the maximum likelihood. During this phase the likelihood of the trees increases steadily. In the second phase, called stationarity, the program explores the parameter space around the maximum likelihood. During stationarity the likelihood seams to vary stochastically around a mean value. The cool thing about an MCMC is that when it is in stationarity it samples the parameter values in a proportion that approximates the posterior probability. That is to say, if given your data and your model there is a 20% chance that Tree A is the right tree, then in stationarity a MCMC will produce that tree approximately 20% of the time. This is true not only for trees, but for all the parameters. Thus you can generate a distribution for the value of any parameter. It makes this approximation without holding any of the other parameters constant, but instead integrating over all values of those parameters. Of course this only works if your model is correct, your priors are correct and you are actually in stationarity for long enough. It is not always easy to tell if you are in stationarity, or how long ‘long enough’ is. Today we will explore Bayesian phylogenetics as discussed in lecture by running analyses and interpreting results. The goals of the lab are the following: I. Adding a MrBayes block to a nexus file II. Conduct a Bayesian analysis III. Analyze chain diagnostics and “burn-in” IV. Summarize parameters from the posterior probability distribution V. Generate a tree with posterior probability values MrBayes is available free in Mac, PC or Unix from: http://mrbayes.csit.fsu.edu/index.php The program comes with example data that we’ll use for the following exercises. We’ll use PAUP or a text editor to edit data matrices and EXCEL to analyze results from the Bayesian analysis. I. Adding a MrBayes block to a nexus file A MrBayes block is a string of commands at the end of a data matrix file that tells the MrBayes program what to do. In the MrBayes block you can specify the model you want to use, your prior distributions, the length of the analysis, the number of samples to keep, etc. 1
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Each line must end with a “ ; ”. Once written, you simply have to execute your matrix in the MrBayes program and it will do the rest. The alternative is to execute your data matrix in MrBayes and enter the commands there. The commands are the same no matter where you enter them. 1.
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11_Bayeslab - Integrative Biology 200A PRINCIPLES OF...

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