32 Questions
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
What is impossible to calculate analytically in real instances of phylogenetic tree inference?
The posterior probability
What does MCMC sampling time spend sampling a particular parameter value depend on?
Proportional to the posterior probability of that parameter value
What is the main focus of computational molecular microbiology course (MBIO 4700)?
Working with sequences and phylogenetic analysis
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?
Maximum likelihood
Which method in phylogenetic analysis focuses on inferring evolutionary relationships based on the principle of minimizing the total amount of change or evolutionary events?
Maximum parsimony methods
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?
Maximum likelihood
Which method in phylogenetic analysis uses algorithms to estimate branch lengths and topology based on sequence dissimilarities?
Distance methods
'Bootstrap' in phylogenetic analysis is used for:
Estimating the reliability of phylogenetic trees
In Bayesian phylogenetic analysis, what is used to summarize probabilities and tree topologies to get consensus trees?
Posterior probabilities
In phylogenetics, what does 'MCMC' stand for?
Markov Chain Monte Carlo
Which software is specifically mentioned for preparing input for BEAST in phylogenetic analysis?
BEAUti
In phylogenetic analysis, which method focuses on inferring evolutionary relationships based on the principle of minimizing the total amount of change or evolutionary events?
Maximum parsimony methods
What is the goal of obtaining the posterior probability distribution in Bayesian phylogenetic analysis?
To summarize probabilities and tree topologies to get consensus trees
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?
Maximum likelihood
'Bootstrap' in phylogenetic analysis is used for:
Assessing the reliability of a phylogenetic tree
'MCMC' in phylogenetics stands for:
Monte Carlo Markov Chain
'BEAST' in phylogenetic analysis is specifically mentioned for calculating:
Evolutionary rates and molecular clocks
In phylogenetic analysis, what does 'MCMC sampling time spend sampling a particular parameter value depend on?
The prior distribution of the parameter value
Which software is mentioned for preparing input for BEAST in phylogenetic analysis?
BEAUti
What is impossible to calculate analytically in real instances of phylogenetic tree inference?
Posterior probabilities
'MrBayes' software is specifically mentioned for which type of analysis?
Bayesian analysis
In Bayesian phylogenetic analysis, what does the MCMC sampling time spend sampling a particular parameter value depend on?
The posterior probability of that parameter value
What is the goal of obtaining the posterior probability distribution in Bayesian phylogenetics?
To obtain the final result of the analysis based on the prior, the data, and the model
What is impossible to calculate analytically in real instances of phylogenetic tree inference?
The posterior probability distribution
Which method in phylogenetic analysis focuses on inferring evolutionary relationships based on the principle of minimizing the total amount of change or evolutionary events?
Parsimony method
'Bootstrap' in phylogenetic analysis is used for:
Assessing the reliability of a phylogenetic tree
Which software is specifically mentioned for preparing input for BEAST in phylogenetic analysis?
BEAUti
Which method in phylogenetic analysis uses algorithms to estimate branch lengths and topology based on sequence dissimilarities?
Maximum likelihood method
What does 'MCMC' stand for in phylogenetics?
Markov Chain Monte Carlo
What is the main focus of computational molecular microbiology course (MBIO 4700)?
Working with sequences and sequence databases
In Bayesian phylogenetic analysis, what is used to summarize probabilities and tree topologies to get consensus trees?
Posterior probability distribution
Test your knowledge of Computational Molecular Microbiology including working with sequences, sequence databases, sequence comparison, alignments, and phylogenetic trees. The quiz may cover topics such as Pairwise alignment, Multiple sequence alignment, and Bayes’ theorem.
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