Bioinformatics Practice Test 7

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

False

True

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

True

False

3. Which of the following is incorrect statement about Tree-Searching Methods?

Parsimony method examines all possible tree topologies to find the maximally parsimonious tree

It starts by building a three taxa unrooted tree, for which only one topology is available

The choice of the first three taxa can be random

This is different than exhaustive search method

4. Which of the following is incorrect about nonparametric bootstrapping?

The most supported branching patterns are the percentage of appearance of a particular clade

The most supported branching patterns shown at each node are labeled with bootstrap values

This test doesn’t provide a measure for evaluating the confidence levels of the tree topology

All the bootstrapped trees are summarized into a consensus tree based on a majority rule

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

False

True

6. Which of the following is untrue regarding the programs for analysis of nucleic acid sequences?

DNAPENNY can analyze sequences up to 11 or 12

Compatibility criterion is not involved in DNACOMP

DNAPARS treats gaps as a fifth nucleotide state

DNAPENNY performs parsimonious phylogenies by branch-and-bound search

7. Which of the following is untrue about distance based methods?

The computed evolutionary distances can be used to construct a matrix of distances between all individual pairs of taxa

Clustering is the only method among the algorithms for the distance-based tree-building method

The clustering-type algorithms compute a tree based on a distance matrix starting from the most similar sequence pairs

Based on the pairwise distance scores in the matrix, a phylogenetic tree can be constructed for all the taxa involved

8. Which of the following is untrue regarding the maximum parsimony method?

This method is used for sequences that are quite similar

This method is used for large numbers of sequences

The analysis steps are continued for every position in the sequence alignment

Those trees that produce the smallest number of changes overall for all sequence positions are identified

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

False

True

10. 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 _____

randomly, vertical, different lengths

randomly, horizontal, same length

specifically, vertical, different lengths

randomly, vertical, same length