Phylogenetic Methods And Programs(Bioinformatics ) Questions and Answers

Question 1. Which of the following is incorrect about Bootstrapping?
  1.    It is a statistical technique that tests the sampling errors of a phylogenetic tree
  2.    It does the tests by repeatedly sampling trees through slightly perturbed datasets
  3.    A newly constructed tree is not biased at all
  4.    The robustness of the original tree can be assessed here
Explanation:-
Answer: Option C. -> A newly constructed tree is not biased at all
Answer: (c).A newly constructed tree is not biased at all
Question 2. A truly robust phylogenetic relationship should have enough characters to support the relationship even if the dataset is perturbed in such away.
  1.    True
  2.    False
  3.    May be True or False
  4.    Can't say
Explanation:-
Answer: Option A. -> True
Answer: (a).True
Question 3. Which of the following is incorrect about Caveats?
  1.    Unusually high GC content in the original dataset is the potential cause for generating biased trees
  2.    Unusually accelerated evolutionary rates is the potential cause for generating biased trees
  3.    Unusually accelerated evolutionary rates is the potential cause for generating biased bootstrap estimates
  4.    Not a large number of bootstrap re-sampling steps are needed to achieve yielding results
Explanation:-
Answer: Option D. -> Not a large number of bootstrap re-sampling steps are needed to achieve yielding results
Answer: (d).Not a large number of bootstrap re-sampling steps are needed to achieve yielding results
Question 4. Which of the following is incorrect about nonparametric bootstrapping?
  1.    A new multiple sequence alignment of the same length is generated with random duplication of some of the sites
  2.    A new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites
  3.    Certain sites are randomly replaced by other existing sites
  4.    Certain sites may appear multiple times, and other sites may not appear at all in the new alignment
Explanation:-
Answer: Option B. -> A new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites
Answer: (b).A new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites
Question 5. Which of the following is incorrect about nonparametric bootstrapping?
  1.    All the bootstrapped trees are summarized into a consensus tree based on a majority rule
  2.    The most supported branching patterns shown at each node are labeled with bootstrap values
  3.    The most supported branching patterns are the percentage of appearance of a particular clade
  4.    This test doesn’t provide a measure for evaluating the confidence levels of the tree topology
Explanation:-
Answer: Option D. -> This test doesn’t provide a measure for evaluating the confidence levels of the tree topology
Answer: (d).This test doesn’t provide a measure for evaluating the confidence levels of the tree topology
Question 6. Which of the following is incorrect statement?
  1.    In this method one half of the sites in a dataset are randomly deleted
  2.    It creates datasets half as long as the original
  3.    Each new dataset is subjected to phylogenetic tree construction using the different methods as the original
  4.    One criticism of this approach is that the size of datasets has been changed into one half and that the datasets are no longer considered replicates
Explanation:-
Answer: Option C. -> Each new dataset is subjected to phylogenetic tree construction using the different methods as the original
Answer: (c).Each new dataset is subjected to phylogenetic tree construction using the different methods as the original
Question 7. In Shimodaira–Hasegawa Test, The degree of freedom used for the analysis depends on the substitution model used. It relies on the following test formula d = 2(ln LA – ln LB) = 2 ln(LA/LB). Here, is the log likelihood ratio score and ln LA and ln LB are likelihood scores for tree A and tree B, respectively.
  1.    True
  2.    False
  3.    May be True or False
  4.    Can't say
Explanation:-
Answer: Option A. -> True
Answer: (a).True
Question 8. In phylogenetic analysis, it is also important to test whether two competing tree topologies can be distinguished and whether one tree is significantly better than the other.
  1.    True
  2.    False
  3.    May be True or False
  4.    Can't say
Explanation:-
Answer: Option A. -> True
Answer: (a).True
Question 9. Which of the following is incorrect about Bayesian Simulation?
  1.    It does not require bootstrapping
  2.    It requires bootstrapping
  3.    The MCMC procedure itself involves thousands or millions of steps of resampling
  4.    Posterior probabilities are assigned at each node of a best Bayesian tree as statistical support
Explanation:-
Answer: Option B. -> It requires bootstrapping
Answer: (b).It requires bootstrapping
Question 10. The KH test sets out to test the null hypothesis that the two competing tree topologies are not significantly different.
  1.    True
  2.    False
  3.    May be True or False
  4.    Can't say
Explanation:-
Answer: Option A. -> True
Answer: (a).True
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