Q. Two more recent uses of phylogenetic analysis are to analyze ______ and to trace the evolutionary history of specific genes. Which of the following could not be the correct blank?

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Q. The traditional use of phylogenetic analysis is to discover evolutionary relationships among species.

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Q. A common recommendation is to use at least two of the methods—maximum parsimony, distance, or maximum likelihood, for the analysis.

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Q. In the final steps of the bootstrap method, the _____ the decay value, the _______ significant the original branches.

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Q. In the bootstrap method, for branches in the predicted tree topology to be significant, the resampled data sets should frequently predict the same branches.

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Q. In the bootstrap method, the data are resampled by _____ choosing _____ columns from the aligned sequences to produce, in effect, a new sequence alignment of the _____

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Q. The choice of a suitable multiple sequence alignment method depends on the degree of variation among the sequences.

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Q. For sequences that have ________ a phylogenetic analysis is __________

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Q. Phylogenetic analysis of a set of sequences that aligns ______ is straightforward because the positions that correspond in the sequences can be readily identified in a ______ of the sequences.

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Q. A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

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Q. A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

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Q. Once all positions in the sequence alignment have been examined, the likelihoods given by each column in the alignment for each tree are _____ to give the likelihood of the tree.

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Q. Which of the following is wrong statement about the maximum likelihood method’s steps?

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Q. Which of the following is wrong statement about DNAML and DNAMLK?

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Q. Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.

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Q. The main disadvantage of maximum likelihood methods is that they are _____

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Q. The maximum likelihood method can be used to explore relationships among more diverse sequences, conditions that are not well handled by maximum parsimony methods.

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Q. In about the maximum likelihood approach, for each tree, the number of sequence changes or mutations that may have occurred to give the sequence variation is considered.

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Q. Which of the following is wrong statement about the maximum likelihood approach?

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Q. Neighbor-joining chooses the sequences that should be joined to give the best least squares estimates of the branch lengths that most closely reflect the actual distances between the sequences.

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