UW-Madison BOTANY 563 - Computer Lab 10 - Bayesian Analysis II (4 pages)

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Computer Lab 10 - Bayesian Analysis II



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Computer Lab 10 - Bayesian Analysis II

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Pages:
4
School:
University of Wisconsin, Madison
Course:
Botany 563 - Phylogenetic Analysis of Molecular Data

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N I Cacho D A Baum 2009 Phylogenetic Analysis of Molecular Data Botany 563 Computer Lab 10 Bayesian Analysis II For useful information refer to the MrBayes manual which you can find at http mrbayes csit fsu edu manual php Learning objective Exploring the posterior to assess support for alternative hypotheses in a Bayesian framework Dataset pereskiabay4 nex A few weeks ago you rejected monophyly of Pereskia based on a Templeton test We will go back to the same dataset now in a Bayesian framework to investigate if there is any support for monophyly Task 1a Run a Bayesian MCMC analysis of this data To do this you only need to analyze the dataset in the file pereskiabay4 nex Look at each command line at the end of the bayes block and make sure you know what it is telling MrBayes to do BEGIN mrbayes log start filename pereskiabay4 log append CHARSET phyC 5018 6150 CHARSET chlormito 1 5017 partition genome 2 chlormito phyC set partition genome lset applyto 1 nst 2 lset applyto 2 nst 6 rates invgamma mcmcp ngen 10000 temp 0 2 nruns 2 nchains 4 samplefreq 10 savebrlens yes showmodel END To run the analysis TYPE mcmc Q How many samples lines should there be in the p file for this analysis Explain Q Is there good mixing of the chains What are the pertinent values that tell you this If your answer is negative for the previous question how would you improve the mixing 1 N I Cacho D A Baum 2009 1b You can try improving the mixing on your own if so briefly describe what you did and whether it worked Alternatively skip over this section and use the files in the folder pereskia7 which were generated with good mixing for the rest of your analyses 2 N I Cacho D A Baum 2009 Once you have good mixing Task 2 Determine an appropriate burnin and summarize your results sump sumt commands Report the burnin used How did you decide on this value How many trees topologies are there in the sample from the posterior distribution and in the 99 credibility interval Task 3 Assessing support for



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