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Bayesian inference with MrBayes Molecular Phylogenetics – exercise

Bayesian inference with MrBayes Molecular Phylogenetics – exercise. 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 .

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Bayesian inference with MrBayes Molecular Phylogenetics – exercise

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  1. BayesianinferencewithMrBayesMolecularPhylogenetics – exercise

  2. 1. MrBayes 1.1 Overview on MrBayes • ImplementstheMetropolis-Hastings-Green-algorithm. • Analysescanbestartedfromtheinternalcommandline (just like in PAUP*). • The helpcommanddisplays a listofavailablecommands. • help <command>displayshelpto a certaincommend. • More informationunderhttp://mrbayes.sourceforge.net/mb3.2_manual.pdf • Command referenceunderhttp://mrbayes.sourceforge.net/Help/

  3. 1. MrBayes 1.2 Importantcommandstostart an analysis • execute<alignmentFile>: Reads alignmentdatafrom a file (e.g. Nexus). • lset: Can beusedtosetthemodelparameters (e.g. nst=6 rates=invgammasetsthe GTR+I+G model) • mcmc: Starts an MCMC analysiswiththeloadedalignment. • ngen: The numberofgenerationsforthechaintorun. • samplefreq: The frequencyofgenerationswhen a treeshallbewrittentothe log file • printfreq: The frequencytoprintinformation on thecurrentruntothecommandline. • diagnfreq: The frequencytoanalizethecurrentprocess (e.g. themeasure of the similarity of the current tree samples). • savebrlens: Specifyyeshere, ifbranchlengthsshallbesaved. • nchains: Specifiesthenumberof parallel chains(defaultis 4).

  4. 1. MrBayes 1.3 Importantcommandsto finish an analysis • plot: Plots thedeveopmentof an estimatedparameterover time (The parametertobedisplayedcanbeselected.) • sump: Summarize samples of model parameters (section 2.2.8 in manual) • sumt: Summarizethetreesamples

  5. 1. MrBayes 1.4 Running an analysis • During an analysisthecurrentln(linkelihood) of all chainsareprinted out. diagnosisoutput run 1 run 2 coldchain heatedchains

  6. 1. MrBayes 1.5 Continuingtheanalysis • After thespecifiednumberofgenerationshasbeenreached, youareasked, ifyouwanttocontinuethechain. • The averagedeviationofsplitfrequenciesshouldbebelow 0.01 in ordertostopthechain

  7. 1. MrBayes 1.6 Output files • MrBayesproducesseveraloutputfiles in yourworkingdirectory • run1.pandrun2.pcontainthedevelopmentofthemodelparametersduringthechain • Can beopened e.g. in Excel • run1.tand run2.tcontain 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.

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