Computational Molecular Microbiology Quiz
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Questions and Answers

In Bayesian phylogenetics, what is the goal of obtaining the posterior probability distribution?

  • To obtain the final result of the analysis based on the prior, the data, and the model (correct)
  • To determine the evolutionary distance between species
  • To estimate the number of iterations for MCMC sampling
  • To calculate the likelihood of a specific phylogenetic tree

    • What is impossible to calculate analytically in real instances of phylogenetic tree inference?

  • The pairwise alignment score
  • The posterior probability (correct)
  • The sequence databases
  • The evolutionary rate of species

    • What does MCMC sampling time spend sampling a particular parameter value depend on?

  • Proportional to the posterior probability of that parameter value (correct)
  • Proportional to the number of species in the phylogenetic tree
  • Proportional to the sequence comparison score
  • Proportional to the outgroup species' characteristics

    • What is the main focus of computational molecular microbiology course (MBIO 4700)?

    <p>Working with sequences and phylogenetic analysis</p> Signup and view all the answers

    In phylogenetic analysis, which method aims to find the tree that fits the data by evaluating tree topologies until a set of trees are generated with overall 'good' probabilities?

    <p>Maximum likelihood</p> Signup and view all the answers

    Which method in phylogenetic analysis focuses on inferring evolutionary relationships based on the principle of minimizing the total amount of change or evolutionary events?

    <p>Maximum parsimony methods</p> Signup and view all the answers

    Which method in phylogenetic analysis involves constructing a tree that maximizes the probability of observing the given DNA/protein sequence data under a particular model of evolution?

    <p>Maximum likelihood</p> Signup and view all the answers

    Which method in phylogenetic analysis uses algorithms to estimate branch lengths and topology based on sequence dissimilarities?

    <p>Distance methods</p> Signup and view all the answers

    'Bootstrap' in phylogenetic analysis is used for:

    <p>Estimating the reliability of phylogenetic trees</p> Signup and view all the answers

    In Bayesian phylogenetic analysis, what is used to summarize probabilities and tree topologies to get consensus trees?

    <p>Posterior probabilities</p> Signup and view all the answers

    In phylogenetics, what does 'MCMC' stand for?

    <p>Markov Chain Monte Carlo</p> Signup and view all the answers

    Which software is specifically mentioned for preparing input for BEAST in phylogenetic analysis?

    <p>BEAUti</p> Signup and view all the answers

    In phylogenetic analysis, which method focuses on inferring evolutionary relationships based on the principle of minimizing the total amount of change or evolutionary events?

    <p>Maximum parsimony methods</p> Signup and view all the answers

    What is the goal of obtaining the posterior probability distribution in Bayesian phylogenetic analysis?

    <p>To summarize probabilities and tree topologies to get consensus trees</p> Signup and view all the answers

    Which method in phylogenetic analysis involves constructing a tree that maximizes the probability of observing the given DNA/protein sequence data under a particular model of evolution?

    <p>Maximum likelihood</p> Signup and view all the answers

    'Bootstrap' in phylogenetic analysis is used for:

    <p>Assessing the reliability of a phylogenetic tree</p> Signup and view all the answers

    'MCMC' in phylogenetics stands for:

    <p>Monte Carlo Markov Chain</p> Signup and view all the answers

    'BEAST' in phylogenetic analysis is specifically mentioned for calculating:

    <p>Evolutionary rates and molecular clocks</p> Signup and view all the answers

    In phylogenetic analysis, what does 'MCMC sampling time spend sampling a particular parameter value depend on?

    <p>The prior distribution of the parameter value</p> Signup and view all the answers

    Which software is mentioned for preparing input for BEAST in phylogenetic analysis?

    <p>BEAUti</p> Signup and view all the answers

    What is impossible to calculate analytically in real instances of phylogenetic tree inference?

    <p>Posterior probabilities</p> Signup and view all the answers

    'MrBayes' software is specifically mentioned for which type of analysis?

    <p>Bayesian analysis</p> Signup and view all the answers

    In Bayesian phylogenetic analysis, what does the MCMC sampling time spend sampling a particular parameter value depend on?

    <p>The posterior probability of that parameter value</p> Signup and view all the answers

    What is the goal of obtaining the posterior probability distribution in Bayesian phylogenetics?

    <p>To obtain the final result of the analysis based on the prior, the data, and the model</p> Signup and view all the answers

    What is impossible to calculate analytically in real instances of phylogenetic tree inference?

    <p>The posterior probability distribution</p> Signup and view all the answers

    Which method in phylogenetic analysis focuses on inferring evolutionary relationships based on the principle of minimizing the total amount of change or evolutionary events?

    <p>Parsimony method</p> Signup and view all the answers

    'Bootstrap' in phylogenetic analysis is used for:

    <p>Assessing the reliability of a phylogenetic tree</p> Signup and view all the answers

    Which software is specifically mentioned for preparing input for BEAST in phylogenetic analysis?

    <p>BEAUti</p> Signup and view all the answers

    Which method in phylogenetic analysis uses algorithms to estimate branch lengths and topology based on sequence dissimilarities?

    <p>Maximum likelihood method</p> Signup and view all the answers

    What does 'MCMC' stand for in phylogenetics?

    <p>Markov Chain Monte Carlo</p> Signup and view all the answers

    What is the main focus of computational molecular microbiology course (MBIO 4700)?

    <p>Working with sequences and sequence databases</p> Signup and view all the answers

    In Bayesian phylogenetic analysis, what is used to summarize probabilities and tree topologies to get consensus trees?

    <p>Posterior probability distribution</p> Signup and view all the answers

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