Bayesian inference with MrBayes Molecular Phylogenetics – exercise

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Presentation transcript:

Bayesian inference with MrBayes Molecular Phylogenetics – exercise

1. MrBayes 1.1 Overview on MrBayes Implements the Metropolis-Hastings-Green-algorithm. Analyses can be started from the internal command line (just like in PAUP*). The help command displays a list of available commands. help <command> displays help to a certain commend. More information under http://mrbayes.sourceforge.net/mb3.2_manual.pdf Command reference under http://mrbayes.sourceforge.net/Help/

1.2 Important commands to start an analysis 1. MrBayes 1.2 Important commands to start an analysis execute <alignmentFile>: Reads alignment data from a file (e.g. Nexus). lset: Can be used to set the model parameters (e.g. nst=6 rates=invgamma sets the GTR+I+G model) mcmc: Starts an MCMC analysis with the loaded alignment. ngen: The number of generations for the chain to run. samplefreq: The frequency of generations when a tree shall be written to the log file printfreq: The frequency to print information on the current run to the command line. diagnfreq: The frequency to analize the current process (e.g. the measure of the similarity of the current tree samples). savebrlens: Specify yes here, if branch lengths shall be saved. nchains: Specifies the number of parallel chains (default is 4).

1.3 Important commands to finish an analysis 1. MrBayes 1.3 Important commands to finish an analysis plot: Plots the deveopment of an estimated parameter over time (The parameter to be displayed can be selected.) sump: Summarize samples of model parameters (section 2.2.8 in manual) sumt: Summarize the tree samples

1. MrBayes 1.4 Running an analysis During an analysis the current ln(linkelihood) of all chains are printed out. run 1 diagnosis output run 2 heated chains cold chain

1.5 Continuing the analysis 1. MrBayes 1.5 Continuing the analysis After the specified number of generations has been reached, you are asked, if you want to continue the chain. The average deviation of split frequencies should be below 0.01 in order to stop the chain

1. MrBayes 1.6 Output files MrBayes produces several output files in your working directory run1.p and run2.p contain the development of the model parameters during the chain Can be opened e.g. in Excel run1.t and run2.t contain the tree samples collected during the chain In NEXUS format Can be opened with TreeGraph 2 (or other tree editors) After calling sumt, the result tree is contained in the con-file.