Bioinformatics Mcqs

Page No. 61

Which of the following is incorrect statement about Maximum Parsimony Method?


aBy cutting off the unnecessary variables, model development may become difficult, and there may be more chances of introducing inconsistencies, ambiguities, and redundancies, hence, the name Occam’s razor

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bIn dealing with problems that may have an infinite number of possible solutions, choosing the simplest model may help to ‘cut off’ those variables that are not really necessary to explain the phenomenon

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cThis method chooses a tree that has the fewest evolutionary changes or shortest overall branch lengths

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d It is based on a principle related to a medieval philosophy called Occam’s razor

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View Answer By cutting off the unnecessary variables, model development may become difficult, and there may be more chances of introducing inconsistencies, ambiguities, and redundancies, hence, the name Occam’s razor

Which of the following is incorrect statement about Character-based methods?


aThey are also called discrete methods

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bThey are based directly on the sequence characters rather than on pairwise distances

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cThey doesn’t count mutational events accumulated on the sequences

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dThey may avoid the loss of information when characters are converted to distances

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View Answer They doesn’t count mutational events accumulated on the sequences

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.


aTrue

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bFalse

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ceither true and false

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dnona of these

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View Answer True

The KH test sets out to test the null hypothesis that the two competing tree topologies are not significantly different.


aTrue

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b False

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ceither true and false

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dnone of these

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View Answer True

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.


a True

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bFalse

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ceither true and false

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dnone of these

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View Answer True

Which of the following is incorrect about Bayesian Simulation?


aIt does not require bootstrapping

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b It requires bootstrapping

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c The MCMC procedure itself involves thousands or millions of steps of resampling

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dPosterior probabilities are assigned at each node of a best Bayesian tree as statistical support

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View Answer It requires bootstrapping

Which of the following is incorrect statement?


aIn this method one half of the sites in a dataset are randomly deleted

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bIt creates datasets half as long as the original

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cEach new dataset is subjected to phylogenetic tree construction using the different methods as the original

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dOne 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

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View Answer Each new dataset is subjected to phylogenetic tree construction using the different methods as the original

Which of the following is incorrect about Caveats?


a Unusually high GC content in the original dataset is the potential cause for generating biased trees

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b Unusually accelerated evolutionary rates is the potential cause for generating biased trees

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cUnusually accelerated evolutionary rates is the potential cause for generating biased bootstrap estimates

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d Not a large number of bootstrap re-sampling steps are needed to achieve yielding results

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View Answer Not a large number of bootstrap re-sampling steps are needed to achieve yielding results

Which of the following is incorrect about nonparametric bootstrapping?


aA new multiple sequence alignment of the same length is generated with random duplication of some of the sites

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bA new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites

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c Certain sites are randomly replaced by other existing sites

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dCertain sites may appear multiple times, and other sites may not appear at all in the new alignment

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View Answer A new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites

A truly robust phylogenetic relationship should have enough characters to support the relationship even if the dataset is perturbed in such away.


aTrue

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bFalse

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ceither true and false

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dnone of these

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View Answer True

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