The Maximum Likelihood Approach MCQ

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• 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?
  ক

  The basis of this method is to devise a scheme for introducing substitutions, insertions, and gaps into sequences

  খ

  The basis of this method is to provide a probability that each of these changes occurs over certain periods of evolutionary time

  গ

  Given each of these predicted changes, the method examines all the possible combinations of mutations to change one sequence into another

  ঘ

  Multiple combinations are selected that will be the most likely over time
• 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.
  ক

  multiplied

  খ

  added

  গ

  divided

  ঘ

  squared
• Which of the following is wrong statement about the maximum likelihood method’s steps?
  ক

  It starts with an evolutionary model of sequence change that provides estimates of rates of substitution of one base for another

  খ

  In the beginning there is an evolutionary model of sequence change that provides estimates of transitions and transversions in a set of nucleic acid sequences

  গ

  The rates of all possible substitutions are chosen so that the base composition differs

  ঘ

  The set of sequences is then aligned
• Which of the following is wrong statement about DNAML and DNAMLK?
  ক

  PHYLIP includes mentioned two programs for this maximum likelihood analysis

  খ

  DNAML estimates phylogenies from nucleotide sequences by the maximum likelihood method

  গ

  DNAMLK estimates phylogenies in the same manner as DNAML

  ঘ

  DNAMLK estimates phylogenies without molecular clock
• Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.
  ক

  True

  খ

  False
• The main disadvantage of maximum likelihood methods is that they are _____
  ক

  mathematically less folded

  খ

  mathematically less complex

  গ

  computationally lucid

  ঘ

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

  True

  খ

  False
• 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.
  ক

  True

  খ

  False
• Which of the following is wrong statement about the maximum likelihood approach?
  ক

  This method doesn’t always involve probability calculations

  খ

  It finds a tree that best accounts for the variation in a set of sequences

  গ

  The method is similar to the maximum parsimony method

  ঘ

  The analysis is performed on each column of a multiple sequence alignment