Bioinformatics Mock Test 7

10%

Question 1 of 10

1. In PHYML, The tree searching _____ when the total ML score no longer ______

stops, increases

ceases, increases

terminates, decreases

stops, decreases

Question 1 of 10

Question 2 of 10

2. For studying the evolution of ________ divergent groups of organisms, one may choose either ______ nucleotide sequences, such as ribosomal RNA or protein sequences.

more widely, rapidly evolving

more widely, slowly evolving

less widely, slowly evolving

less widely, rapidly evolving

Question 2 of 10

Question 3 of 10

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

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

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

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

In 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

Question 3 of 10

Question 4 of 10

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

True

False

Question 4 of 10

Question 5 of 10

5. Sometimes a tree-building method may result in several equally optimal trees. A consensus tree can be built by showing the commonly resolved bifurcating portions and collapsing the ones that disagree among the trees, which results in a polytomy.

False

True

Question 5 of 10

Question 6 of 10

6. Which of the following is incorrect about Bootstrapping?

A newly constructed tree is not biased at all

It is a statistical technique that tests the sampling errors of a phylogenetic tree

The robustness of the original tree can be assessed here

It does the tests by repeatedly sampling trees through slightly perturbed datasets

Question 6 of 10

Question 7 of 10

7. Which of the following is untrue regarding the Distance analysis programs in PHYLIP?

FITCH uses the Fitch-Margoliash method

NEIGHBOR estimates phylogenies using the neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA)

FITCH estimates a phylogenetic tree assuming additivity of branch lengths

FITCH assumes a molecular clock but KITSCH does not

Question 7 of 10

Question 8 of 10

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

True

False

Question 8 of 10

Question 9 of 10

9. PAUP is a Macintosh program (UNIX version available in the GCG package) with a very user-friendly graphical interface.

False

True

Question 9 of 10

Question 10 of 10

10. 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.

multiplied

added

squared

divided

Question 10 of 10