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Bioinformatics Practice Test Questions: Phylogenetic Tree Construction Methods and Programs
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Phylogenetic trees can be constructed using three main methods: Distance-based methods: Such as neighbor-joining. These methods calculate evolutionary distances between sequences using substitution models. The distance matrix is then used to construct the phylogenetic tree. Parsimony-based methods: Such as maximum parsimony. Character-based methods: Such as maximum likelihood or Bayesian inference. This method is also called the discrete method because it is based directly on the sequence characters. Phylogenetic trees can be represented in three forms: Phylogram, Dendrogram,... Show more
Bioinformatics Practice Test Questions: Phylogenetic Tree Construction Methods and Programs
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25 Questions

1. Which of the following is incorrect about Bootstrapping?
2. Which of the following is incorrect about nonparametric bootstrapping?
3. Which of the following is wrong statement about the maximum likelihood approach?
4. MrBayes is a Bayesian phylogenetic inference program.
5. Which of the following is untrue about the Optimality-Based Methods?
6. Because these ancestral character states are not known directly, multiple possible solutions may exist. In this case, the parsimony principle applies to choose the character states that result in a minimum number of substitutions.
7. Which of the following is incorrect statement about Tree-Searching Methods?
8. In the Neighbor Joining step, The UPGMA method uses unweighted distances and assumes that all taxa have constant evolutionary rates.
9. In a heuristic tree search, only a small subset of all possible trees is examined.
10. Which of the following is untrue regarding the maximum parsimony method?
11. The traditional use of phylogenetic analysis is to discover evolutionary relationships among species.
12. 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?
13. In the bootstrap method, for branches in the predicted tree topology to be significant, the resampled data sets should frequently predict the same branches.
14. Which of the following is incorrect about Bayesian Simulation?
15. The unweighted method treats all mutations as equivalent.
16. Parsimony can give ________ information when rates of sequence change _______ in the different branches of a tree that are represented by the sequence data.
17. Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.
18. In PAUP, The distance options include NJ, ME, FM, and UPGMA.
19. Phylip stands for Phylogenetic inference package (by Joe Felsenstein).
20. Which of the following is untrue about the Unweighted Pair Group Method Using Arithmetic Average?
21. The tree construction process is somewhat similar to that used UPGMA.
22. The branch-and-bound method starts building trees in a similar way as in the exhaustive method.
23. A truly robust phylogenetic relationship should have enough characters to support the relationship even if the dataset is perturbed in such away.
24. PROTPARS counts the minimum number of mutations to change a codon for the first amino acid into a codon for the second amino acid, but only scores those mutations in the mutational path that actually change the amino acid.
25. The KH test sets out to test the null hypothesis that the two competing tree topologies are not significantly different.

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